From 8129fe7cdcdbf1aca7c5d01230c2f4ff3c5f1031 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Apr 2023 14:26:01 +0000 Subject: [PATCH 001/264] Template update for nf-core/tools version 2.8 --- .editorconfig | 2 +- .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 3 +- .github/workflows/awsfulltest.yml | 2 +- .github/workflows/awstest.yml | 2 +- .github/workflows/branch.yml | 2 +- .github/workflows/clean-up.yml | 24 ++++ .github/workflows/linting.yml | 2 +- .pre-commit-config.yaml | 5 + CHANGELOG.md | 2 +- README.md | 74 ++++++---- bin/check_samplesheet.py | 3 - conf/base.config | 2 +- conf/igenomes.config | 8 ++ conf/test_full.config | 2 + docs/usage.md | 130 +++++------------- lib/NfcoreSchema.groovy | 4 +- lib/WorkflowMain.groovy | 13 +- lib/WorkflowRnafusion.groovy | 12 +- main.nf | 1 - modules.json | 4 +- modules/local/samplesheet_check.nf | 2 +- .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 2 + modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 3 +- nextflow.config | 31 ++++- tower.yml | 5 + 28 files changed, 195 insertions(+), 159 deletions(-) create mode 100644 .github/workflows/clean-up.yml create mode 100644 .pre-commit-config.yaml create mode 100644 tower.yml diff --git a/.editorconfig b/.editorconfig index b78de6e6..b6b31907 100644 --- a/.editorconfig +++ b/.editorconfig @@ -8,7 +8,7 @@ trim_trailing_whitespace = true indent_size = 4 indent_style = space -[*.{md,yml,yaml,html,css,scss,js,cff}] +[*.{md,yml,yaml,html,css,scss,js}] indent_size = 2 # These files are edited and tested upstream in nf-core/modules diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 8ed5ffe6..41c21167 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -45,6 +45,6 @@ body: * Nextflow version _(eg. 22.10.1)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ * OS _(eg. CentOS Linux, macOS, Linux Mint)_ * Version of nf-core/rnafusion _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 6f604f38..5cc076f3 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/rnaf - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/rnafusion _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/rnafusion/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/rnafusion _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index a2fbe1e2..30a9fbbc 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 14762177..be662dd3 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,7 +12,7 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: nf-core/tower-action@v3 + uses: seqeralabs/action-tower-launch@v1 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index ccb7211b..3867817a 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/rnafusion' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnafusion ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/rnafusion ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml new file mode 100644 index 00000000..694e90ec --- /dev/null +++ b/.github/workflows/clean-up.yml @@ -0,0 +1,24 @@ +name: "Close user-tagged issues and PRs" +on: + schedule: + - cron: "0 0 * * 0" # Once a week + +jobs: + clean-up: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." + stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." + close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 858d622e..888cb4bc 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.7" + python-version: "3.8" architecture: "x64" - name: Install dependencies diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..0c31cdb9 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,5 @@ +repos: + - repo: https://github.com/pre-commit/mirrors-prettier + rev: "v2.7.1" + hooks: + - id: prettier diff --git a/CHANGELOG.md b/CHANGELOG.md index 5bb898b7..5470be26 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.2.0dev - [date] +## v2.3.4 - [date] Initial release of nf-core/rnafusion, created with the [nf-core](https://nf-co.re/) template. diff --git a/README.md b/README.md index aa92b95d..7fef3b59 100644 --- a/README.md +++ b/README.md @@ -8,57 +8,71 @@ [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/rnafusion) -[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rnafusion-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rnafusion)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) ## Introduction - +**nf-core/rnafusion** is a bioinformatics pipeline that ... -**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for Nextflow rnafusion analysis pipeline, part of the nf-core community.. - -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - - - -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results). - -## Pipeline summary + + 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -## Quick Start +## Usage + +> **Note** +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) +> with `-profile test` before running the workflow on actual data. + + - Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. +Now, you can run the pipeline using: - > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. - > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. - > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. - > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. + -4. Start running your own analysis! +```bash +nextflow run nf-core/rnafusion \ + -profile \ + --input samplesheet.csv \ + --outdir +``` - +> **Warning:** +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those +> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). - ```bash - nextflow run nf-core/rnafusion --input samplesheet.csv --outdir --genome GRCh37 -profile - ``` +For more details, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters). -## Documentation +## Pipeline output -The nf-core/rnafusion pipeline comes with documentation about the pipeline [usage](https://nf-co.re/rnafusion/usage), [parameters](https://nf-co.re/rnafusion/parameters) and [output](https://nf-co.re/rnafusion/output). +To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page. +For more details about the output files and reports, please refer to the +[output documentation](https://nf-co.re/rnafusion/output). ## Credits diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py index 11b15572..4a758fe0 100755 --- a/bin/check_samplesheet.py +++ b/bin/check_samplesheet.py @@ -158,9 +158,6 @@ def sniff_format(handle): peek = read_head(handle) handle.seek(0) sniffer = csv.Sniffer() - if not sniffer.has_header(peek): - logger.critical("The given sample sheet does not appear to contain a header.") - sys.exit(1) dialect = sniffer.sniff(peek) return dialect diff --git a/conf/base.config b/conf/base.config index d9c546a1..51042a02 100644 --- a/conf/base.config +++ b/conf/base.config @@ -15,7 +15,7 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' diff --git a/conf/igenomes.config b/conf/igenomes.config index 7a1b3ac6..3f114377 100644 --- a/conf/igenomes.config +++ b/conf/igenomes.config @@ -36,6 +36,14 @@ params { macs_gsize = "2.7e9" blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" } + 'CHM13' { + fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" + bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" + bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" + gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" + gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" + mito_name = "chrM" + } 'GRCm38' { fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" diff --git a/conf/test_full.config b/conf/test_full.config index e2522d72..54ef4afd 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,6 +10,8 @@ ---------------------------------------------------------------------------------------- */ +cleanup = true + params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 977e4b38..06b9bc29 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -71,6 +71,29 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +> The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/rnafusion -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +genome: 'GRCh37' +input: 'data' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -87,6 +110,10 @@ First, go to the [nf-core/rnafusion releases page](https://github.com/nf-core/rn This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. +To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. + +> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. + ## Core Nextflow arguments > **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). @@ -95,7 +122,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. @@ -119,8 +146,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) - `charliecloud` - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) +- `apptainer` + - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `conda` - - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. + - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. ### `-resume` @@ -138,102 +167,19 @@ Specify the path to a specific config file (this is a core Nextflow command). Se Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. -For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue: - -```console -[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1) -Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)' - -Caused by: - Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) - -Command executed: - STAR \ - --genomeDir star \ - --readFilesIn WT_REP1_trimmed.fq.gz \ - --runThreadN 2 \ - --outFileNamePrefix WT_REP1. \ - - -Command exit status: - 137 - -Command output: - (empty) - -Command error: - .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1. -Work dir: - /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb - -Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -``` - -#### For beginners - -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. - -#### Advanced option on process level - -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. -The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. - -```nextflow -process { - withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' { - memory = 100.GB - } -} -``` - -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. - -### Updating containers (advanced users) - -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. - -1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) -2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) -3. Create the custom config accordingly: - - - For Docker: +To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. - ```nextflow - process { - withName: PANGOLIN { - container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +### Custom Containers - - For Singularity: +In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. - ```nextflow - process { - withName: PANGOLIN { - container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0' - } - } - ``` +To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. - - For Conda: +### Custom Tool Arguments - ```nextflow - process { - withName: PANGOLIN { - conda = 'bioconda::pangolin=3.0.5' - } - } - ``` +A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default. -> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch. +To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website. ### nf-core/configs diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy index 33cd4f6e..9b34804d 100755 --- a/lib/NfcoreSchema.groovy +++ b/lib/NfcoreSchema.groovy @@ -2,6 +2,7 @@ // This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. // +import nextflow.Nextflow import org.everit.json.schema.Schema import org.everit.json.schema.loader.SchemaLoader import org.everit.json.schema.ValidationException @@ -83,6 +84,7 @@ class NfcoreSchema { 'stub-run', 'test', 'w', + 'with-apptainer', 'with-charliecloud', 'with-conda', 'with-dag', @@ -177,7 +179,7 @@ class NfcoreSchema { } if (has_error) { - System.exit(1) + Nextflow.error('Exiting!') } } diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 83ded3a4..7674aa79 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -2,6 +2,8 @@ // This file holds several functions specific to the main.nf workflow in the nf-core/rnafusion pipeline // +import nextflow.Nextflow + class WorkflowMain { // @@ -21,7 +23,7 @@ class WorkflowMain { // // Generate help string // - public static String help(workflow, params, log) { + public static String help(workflow, params) { def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" def help_string = '' help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) @@ -34,7 +36,7 @@ class WorkflowMain { // // Generate parameter summary log string // - public static String paramsSummaryLog(workflow, params, log) { + public static String paramsSummaryLog(workflow, params) { def summary_log = '' summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) @@ -49,7 +51,7 @@ class WorkflowMain { public static void initialise(workflow, params, log) { // Print help to screen if required if (params.help) { - log.info help(workflow, params, log) + log.info help(workflow, params) System.exit(0) } @@ -61,7 +63,7 @@ class WorkflowMain { } // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params, log) + log.info paramsSummaryLog(workflow, params) // Validate workflow parameters via the JSON schema if (params.validate_params) { @@ -81,8 +83,7 @@ class WorkflowMain { // Check input has been provided if (!params.input) { - log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" - System.exit(1) + Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'") } } // diff --git a/lib/WorkflowRnafusion.groovy b/lib/WorkflowRnafusion.groovy index f31abbf7..9c2e78c1 100755 --- a/lib/WorkflowRnafusion.groovy +++ b/lib/WorkflowRnafusion.groovy @@ -2,6 +2,7 @@ // This file holds several functions specific to the workflow/rnafusion.nf in the nf-core/rnafusion pipeline // +import nextflow.Nextflow import groovy.text.SimpleTemplateEngine class WorkflowRnafusion { @@ -14,8 +15,7 @@ class WorkflowRnafusion { if (!params.fasta) { - log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." - System.exit(1) + Nextflow.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." } } @@ -61,17 +61,19 @@ class WorkflowRnafusion { def description_html = engine.createTemplate(methods_text).make(meta) return description_html - }// + } + + // // Exit pipeline if incorrect --genome key provided // private static void genomeExistsError(params, log) { if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + + def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + " Currently, the available genome keys are:\n" + " ${params.genomes.keySet().join(", ")}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - System.exit(1) + Nextflow.error(error_string) } } } diff --git a/main.nf b/main.nf index 8cb0a641..b2c34856 100644 --- a/main.nf +++ b/main.nf @@ -4,7 +4,6 @@ nf-core/rnafusion ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Github : https://github.com/nf-core/rnafusion - Website: https://nf-co.re/rnafusion Slack : https://nfcore.slack.com/channels/rnafusion ---------------------------------------------------------------------------------------- diff --git a/modules.json b/modules.json index d7bc9b18..c8d72c8f 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", "installed_by": ["modules"] }, "fastqc": { @@ -17,7 +17,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7", "installed_by": ["modules"] } } diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf index 695bcdb3..9226705d 100644 --- a/modules/local/samplesheet_check.nf +++ b/modules/local/samplesheet_check.nf @@ -5,7 +5,7 @@ process SAMPLESHEET_CHECK { conda "conda-forge::python=3.8.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'quay.io/biocontainers/python:3.8.3' }" + 'biocontainers/python:3.8.3' }" input: path samplesheet diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 3df21765..800a6099 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 60b546a0..c32657de 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,7 +1,9 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - custom + - dump - version tools: - custom: diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 68f66bea..4b604749 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.13" + conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index ebc29b27..f93b5ee5 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: @@ -37,7 +38,7 @@ output: description: MultiQC report file pattern: "multiqc_report.html" - data: - type: dir + type: directory description: MultiQC data dir pattern: "multiqc_data" - plots: diff --git a/nextflow.config b/nextflow.config index eba99080..1becd30e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -78,7 +78,11 @@ try { profiles { - debug { process.beforeScript = 'echo $HOSTNAME' } + debug { + dumpHashes = true + process.beforeScript = 'echo $HOSTNAME' + cleanup = false + } conda { conda.enabled = true docker.enabled = false @@ -86,6 +90,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } mamba { conda.enabled = true @@ -95,14 +100,18 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } docker { docker.enabled = true + docker.registry = 'quay.io' docker.userEmulation = true + conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' @@ -110,31 +119,49 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } podman { podman.enabled = true + podman.registry = 'quay.io' + conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false charliecloud.enabled = false + apptainer.enabled = false } shifter { shifter.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false charliecloud.enabled = false + apptainer.enabled = false } charliecloud { charliecloud.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false + apptainer.enabled = false + } + apptainer { + apptainer.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } gitpod { executor.name = 'local' @@ -193,7 +220,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '2.2.0dev' + version = '2.3.4' doi = '' } diff --git a/tower.yml b/tower.yml new file mode 100644 index 00000000..787aedfe --- /dev/null +++ b/tower.yml @@ -0,0 +1,5 @@ +reports: + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths" From 18673734c6bc5814fc068d5a1392ee61d1e31f94 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 30 Jun 2023 16:15:33 +0000 Subject: [PATCH 002/264] Template update for nf-core/tools version 2.9 --- .github/CONTRIBUTING.md | 1 - .github/ISSUE_TEMPLATE/bug_report.yml | 2 +- .github/workflows/awsfulltest.yml | 11 +- .github/workflows/awstest.yml | 10 +- .github/workflows/ci.yml | 2 +- .gitpod.yml | 5 + CITATIONS.md | 6 + README.md | 6 +- assets/methods_description_template.yml | 12 +- assets/multiqc_config.yml | 4 +- assets/nf-core-rnafusion_logo_light.png | Bin 10989 -> 72629 bytes assets/slackreport.json | 2 +- conf/test_full.config | 2 - docs/usage.md | 6 +- lib/NfcoreSchema.groovy | 530 ------------------------ lib/NfcoreTemplate.groovy | 2 +- lib/WorkflowMain.groovy | 37 -- lib/WorkflowRnafusion.groovy | 45 +- main.nf | 16 + nextflow.config | 52 ++- nextflow_schema.json | 36 +- workflows/rnafusion.nf | 25 +- 22 files changed, 175 insertions(+), 637 deletions(-) delete mode 100755 lib/NfcoreSchema.groovy diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index d4b48eae..975df6cd 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -116,4 +116,3 @@ To get started: Devcontainer specs: - [DevContainer config](.devcontainer/devcontainer.json) -- [Dockerfile](.devcontainer/Dockerfile) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 41c21167..7755ffb4 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -42,7 +42,7 @@ body: attributes: label: System information description: | - * Nextflow version _(eg. 22.10.1)_ + * Nextflow version _(eg. 23.04.0)_ * Hardware _(eg. HPC, Desktop, Cloud)_ * Executor _(eg. slurm, local, awsbatch)_ * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 30a9fbbc..2db9edfa 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters @@ -22,13 +22,18 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} parameters: | { + "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}" } - profiles: test_full,aws_tower + profiles: test_full + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index be662dd3..5ef7e96c 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -12,18 +12,22 @@ jobs: steps: # Launch workflow using Tower CLI tool action - name: Launch workflow via tower - uses: seqeralabs/action-tower-launch@v1 + uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} + revision: ${{ github.sha }} workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} parameters: | { "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-test-${{ github.sha }}" } - profiles: test,aws_tower + profiles: test + - uses: actions/upload-artifact@v3 with: name: Tower debug log file - path: tower_action_*.log + path: | + tower_action_*.log + tower_action_*.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ff58f38e..a6726dd9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -24,7 +24,7 @@ jobs: strategy: matrix: NXF_VER: - - "22.10.1" + - "23.04.0" - "latest-everything" steps: - name: Check out pipeline code diff --git a/.gitpod.yml b/.gitpod.yml index 85d95ecc..25488dcc 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack diff --git a/CITATIONS.md b/CITATIONS.md index b298989b..1d65b743 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,10 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools @@ -31,5 +34,8 @@ - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) + > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241. + - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. diff --git a/README.md b/README.md index 7fef3b59..504929dd 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -66,11 +66,11 @@ nextflow run nf-core/rnafusion \ > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -For more details, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnafusion/usage) and the [parameter documentation](https://nf-co.re/rnafusion/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/rnafusion/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/rnafusion/output). diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 016b3d45..62a8ff4e 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/rnafusion Methods Description" section_href: "https://github.com/nf-core/rnafusion" plot_type: "html" -## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline +## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

Data was processed using nf-core/rnafusion v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

+

Data was processed using nf-core/rnafusion v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

${workflow.commandLine}
+

${tool_citations}

References

    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
    • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
    • +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
    • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
    • +
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • +
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • + ${tool_bibliography}
Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5c8a20b2..d8d63229 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnafusion-methods-description": order: -1000 diff --git a/assets/nf-core-rnafusion_logo_light.png b/assets/nf-core-rnafusion_logo_light.png index 55f385411694bc192b1d6cf172a0c7defcd49d1a..5609a199d523605d536b8c5bb0aae654af1c4a57 100644 GIT binary patch literal 72629 zcmeEt`9IX_`~RRQS?ZKSWhn*~p=96c5GGq9OZHNfecuPCQz(&w!1jG0qM))u18{N;szxKLnntC7*Z0~7*=;B1!jv^4p5Gb_^hQ29NgTYTSd@O|5 zS3HI44fR<@BwC_WweNAg^K`t?ay|Ua^`zuS;o*5X;p5j0nLR_3TdTw-*C$<<{Vk$; z9`%au>-b1%=CCl=x~!Jp!Br{RFpzjKp!3X+Tb;*QRKss@Kb){h^c+@seV?p-3zMBT zv9)Zlu({<`v3Pc z_~QTk@G~L)&kz6ShyTBGp!b^mFYH1%8g&}PE+NMRdy{Rgwkaa9QvrRQY2HJz)6`6H z9;J$!8p?T$p0J;N*Ye!J#ykH8M)iUCxVX5E!@pK|Rzc1t45Gxe-2E^GvsRWhY(8G+ zqQw!LH!;zIl^)J$8$X^IcCItbD!;xEnF(K*M&+X@JSfW~(%%?AjAD}I{FvT)!b;+< zT`3RVvHyDV#tr{F?pFSzX|tN{P8k1QHN6RI-9sVD@-lUEm%l0Eg`Uqb{CpIznVgoC zqUmmd=@Irb{U+;BnnF@S4JpEd=f8=bxA|}L4A?vsm9JMY?xEj%PSrz{(B9T6zCrD{ 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(success) { %>good<% } else { %>danger<%} %>", - "author_name": "sanger-tol/readmapping v${version} - ${runName}", + "author_name": "nf-core/rnafusion v${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/test_full.config b/conf/test_full.config index 54ef4afd..e2522d72 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/docs/usage.md b/docs/usage.md index 06b9bc29..bcf9dd8d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -57,7 +57,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/rnafusion --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run nf-core/rnafusion --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -76,7 +76,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run nf-core/rnafusion -profile docker -params-file params.yaml @@ -88,7 +89,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ``` diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy deleted file mode 100755 index 9b34804d..00000000 --- a/lib/NfcoreSchema.groovy +++ /dev/null @@ -1,530 +0,0 @@ -// -// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. -// - -import nextflow.Nextflow -import org.everit.json.schema.Schema -import org.everit.json.schema.loader.SchemaLoader -import org.everit.json.schema.ValidationException -import org.json.JSONObject -import org.json.JSONTokener -import org.json.JSONArray -import groovy.json.JsonSlurper -import groovy.json.JsonBuilder - -class NfcoreSchema { - - // - // Resolve Schema path relative to main workflow directory - // - public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') { - return "${workflow.projectDir}/${schema_filename}" - } - - // - // Function to loop over all parameters defined in schema and check - // whether the given parameters adhere to the specifications - // - /* groovylint-disable-next-line UnusedPrivateMethodParameter */ - public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') { - def has_error = false - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Check for nextflow core params and unexpected params - def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text - def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') - def nf_params = [ - // Options for base `nextflow` command - 'bg', - 'c', - 'C', - 'config', - 'd', - 'D', - 'dockerize', - 'h', - 'log', - 'q', - 'quiet', - 'syslog', - 'v', - - // Options for `nextflow run` command - 'ansi', - 'ansi-log', - 'bg', - 'bucket-dir', - 'c', - 'cache', - 'config', - 'dsl2', - 'dump-channels', - 'dump-hashes', - 'E', - 'entry', - 'latest', - 'lib', - 'main-script', - 'N', - 'name', - 'offline', - 'params-file', - 'pi', - 'plugins', - 'poll-interval', - 'pool-size', - 'profile', - 'ps', - 'qs', - 'queue-size', - 'r', - 'resume', - 'revision', - 'stdin', - 'stub', - 'stub-run', - 'test', - 'w', - 'with-apptainer', - 'with-charliecloud', - 'with-conda', - 'with-dag', - 'with-docker', - 'with-mpi', - 'with-notification', - 'with-podman', - 'with-report', - 'with-singularity', - 'with-timeline', - 'with-tower', - 'with-trace', - 'with-weblog', - 'without-docker', - 'without-podman', - 'work-dir' - ] - def unexpectedParams = [] - - // Collect expected parameters from the schema - def expectedParams = [] - def enums = [:] - for (group in schemaParams) { - for (p in group.value['properties']) { - expectedParams.push(p.key) - if (group.value['properties'][p.key].containsKey('enum')) { - enums[p.key] = group.value['properties'][p.key]['enum'] - } - } - } - - for (specifiedParam in params.keySet()) { - // nextflow params - if (nf_params.contains(specifiedParam)) { - log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" - has_error = true - } - // unexpected params - def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' - def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() } - def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase() - def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase)) - if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) { - // Temporarily remove camelCase/camel-case params #1035 - def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()} - if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){ - unexpectedParams.push(specifiedParam) - } - } - } - - //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~// - // Validate parameters against the schema - InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream() - JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream)) - - // Remove anything that's in params.schema_ignore_params - raw_schema = removeIgnoredParams(raw_schema, params) - - Schema schema = SchemaLoader.load(raw_schema) - - // Clean the parameters - def cleanedParams = cleanParameters(params) - - // Convert to JSONObject - def jsonParams = new JsonBuilder(cleanedParams) - JSONObject params_json = new JSONObject(jsonParams.toString()) - - // Validate - try { - schema.validate(params_json) - } catch (ValidationException e) { - println '' - log.error 'ERROR: Validation of pipeline parameters failed!' - JSONObject exceptionJSON = e.toJSON() - printExceptions(exceptionJSON, params_json, log, enums) - println '' - has_error = true - } - - // Check for unexpected parameters - if (unexpectedParams.size() > 0) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - println '' - def warn_msg = 'Found unexpected parameters:' - for (unexpectedParam in unexpectedParams) { - warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" - } - log.warn warn_msg - log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" - println '' - } - - if (has_error) { - Nextflow.error('Exiting!') - } - } - - // - // Beautify parameters for --help - // - public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - Integer num_hidden = 0 - String output = '' - output += 'Typical pipeline command:\n\n' - output += " ${colors.cyan}${command}${colors.reset}\n\n" - Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - Integer max_chars = paramsMaxChars(params_map) + 1 - Integer desc_indent = max_chars + 14 - Integer dec_linewidth = 160 - desc_indent - for (group in params_map.keySet()) { - Integer num_params = 0 - String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (group_params.get(param).hidden && !params.show_hidden_params) { - num_hidden += 1 - continue; - } - def type = '[' + group_params.get(param).type + ']' - def description = group_params.get(param).description - def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : '' - def description_default = description + colors.dim + defaultValue + colors.reset - // Wrap long description texts - // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap - if (description_default.length() > dec_linewidth){ - List olines = [] - String oline = "" // " " * indent - description_default.split(" ").each() { wrd -> - if ((oline.size() + wrd.size()) <= dec_linewidth) { - oline += wrd + " " - } else { - olines += oline - oline = wrd + " " - } - } - olines += oline - description_default = olines.join("\n" + " " * desc_indent) - } - group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' - num_params += 1 - } - group_output += '\n' - if (num_params > 0){ - output += group_output - } - } - if (num_hidden > 0){ - output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset - } - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Groovy Map summarising parameters/workflow options used by the pipeline - // - public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') { - // Get a selection of core Nextflow workflow options - def Map workflow_summary = [:] - if (workflow.revision) { - workflow_summary['revision'] = workflow.revision - } - workflow_summary['runName'] = workflow.runName - if (workflow.containerEngine) { - workflow_summary['containerEngine'] = workflow.containerEngine - } - if (workflow.container) { - workflow_summary['container'] = workflow.container - } - workflow_summary['launchDir'] = workflow.launchDir - workflow_summary['workDir'] = workflow.workDir - workflow_summary['projectDir'] = workflow.projectDir - workflow_summary['userName'] = workflow.userName - workflow_summary['profile'] = workflow.profile - workflow_summary['configFiles'] = workflow.configFiles.join(', ') - - // Get pipeline parameters defined in JSON Schema - def Map params_summary = [:] - def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename)) - for (group in params_map.keySet()) { - def sub_params = new LinkedHashMap() - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (params.containsKey(param)) { - def params_value = params.get(param) - def schema_value = group_params.get(param).default - def param_type = group_params.get(param).type - if (schema_value != null) { - if (param_type == 'string') { - if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { - def sub_string = schema_value.replace('\$projectDir', '') - sub_string = sub_string.replace('\${projectDir}', '') - if (params_value.contains(sub_string)) { - schema_value = params_value - } - } - if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { - def sub_string = schema_value.replace('\$params.outdir', '') - sub_string = sub_string.replace('\${params.outdir}', '') - if ("${params.outdir}${sub_string}" == params_value) { - schema_value = params_value - } - } - } - } - - // We have a default in the schema, and this isn't it - if (schema_value != null && params_value != schema_value) { - sub_params.put(param, params_value) - } - // No default in the schema, and this isn't empty - else if (schema_value == null && params_value != "" && params_value != null && params_value != false) { - sub_params.put(param, params_value) - } - } - } - params_summary.put(group, sub_params) - } - return [ 'Core Nextflow options' : workflow_summary ] << params_summary - } - - // - // Beautify parameters for summary and return as string - // - public static String paramsSummaryLog(workflow, params) { - Map colors = NfcoreTemplate.logColours(params.monochrome_logs) - String output = '' - def params_map = paramsSummaryMap(workflow, params) - def max_chars = paramsMaxChars(params_map) - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - if (group_params) { - output += colors.bold + group + colors.reset + '\n' - for (param in group_params.keySet()) { - output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n' - } - output += '\n' - } - } - output += "!! Only displaying parameters that differ from the pipeline defaults !!\n" - output += NfcoreTemplate.dashedLine(params.monochrome_logs) - return output - } - - // - // Loop over nested exceptions and print the causingException - // - private static void printExceptions(ex_json, params_json, log, enums, limit=5) { - def causingExceptions = ex_json['causingExceptions'] - if (causingExceptions.length() == 0) { - def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/ - // Missing required param - if (m.matches()) { - log.error "* Missing required parameter: --${m[0][1]}" - } - // Other base-level error - else if (ex_json['pointerToViolation'] == '#') { - log.error "* ${ex_json['message']}" - } - // Error with specific param - else { - def param = ex_json['pointerToViolation'] - ~/^#\// - def param_val = params_json[param].toString() - if (enums.containsKey(param)) { - def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices" - if (enums[param].size() > limit) { - log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )" - } else { - log.error "${error_msg}: ${enums[param].join(', ')})" - } - } else { - log.error "* --${param}: ${ex_json['message']} (${param_val})" - } - } - } - for (ex in causingExceptions) { - printExceptions(ex, params_json, log, enums) - } - } - - // - // Remove an element from a JSONArray - // - private static JSONArray removeElement(json_array, element) { - def list = [] - int len = json_array.length() - for (int i=0;i - if(raw_schema.keySet().contains('definitions')){ - raw_schema.definitions.each { definition -> - for (key in definition.keySet()){ - if (definition[key].get("properties").keySet().contains(ignore_param)){ - // Remove the param to ignore - definition[key].get("properties").remove(ignore_param) - // If the param was required, change this - if (definition[key].has("required")) { - def cleaned_required = removeElement(definition[key].required, ignore_param) - definition[key].put("required", cleaned_required) - } - } - } - } - } - if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) { - raw_schema.get("properties").remove(ignore_param) - } - if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) { - def cleaned_required = removeElement(raw_schema.required, ignore_param) - raw_schema.put("required", cleaned_required) - } - } - return raw_schema - } - - // - // Clean and check parameters relative to Nextflow native classes - // - private static Map cleanParameters(params) { - def new_params = params.getClass().newInstance(params) - for (p in params) { - // remove anything evaluating to false - if (!p['value']) { - new_params.remove(p.key) - } - // Cast MemoryUnit to String - if (p['value'].getClass() == nextflow.util.MemoryUnit) { - new_params.replace(p.key, p['value'].toString()) - } - // Cast Duration to String - if (p['value'].getClass() == nextflow.util.Duration) { - new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day")) - } - // Cast LinkedHashMap to String - if (p['value'].getClass() == LinkedHashMap) { - new_params.replace(p.key, p['value'].toString()) - } - } - return new_params - } - - // - // This function tries to read a JSON params file - // - private static LinkedHashMap paramsLoad(String json_schema) { - def params_map = new LinkedHashMap() - try { - params_map = paramsRead(json_schema) - } catch (Exception e) { - println "Could not read parameters settings from JSON. $e" - params_map = new LinkedHashMap() - } - return params_map - } - - // - // Method to actually read in JSON file using Groovy. - // Group (as Key), values are all parameters - // - Parameter1 as Key, Description as Value - // - Parameter2 as Key, Description as Value - // .... - // Group - // - - private static LinkedHashMap paramsRead(String json_schema) throws Exception { - def json = new File(json_schema).text - def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') - def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') - /* Tree looks like this in nf-core schema - * definitions <- this is what the first get('definitions') gets us - group 1 - title - description - properties - parameter 1 - type - description - parameter 2 - type - description - group 2 - title - description - properties - parameter 1 - type - description - * properties <- parameters can also be ungrouped, outside of definitions - parameter 1 - type - description - */ - - // Grouped params - def params_map = new LinkedHashMap() - schema_definitions.each { key, val -> - def Map group = schema_definitions."$key".properties // Gets the property object of the group - def title = schema_definitions."$key".title - def sub_params = new LinkedHashMap() - group.each { innerkey, value -> - sub_params.put(innerkey, value) - } - params_map.put(title, sub_params) - } - - // Ungrouped params - def ungrouped_params = new LinkedHashMap() - schema_properties.each { innerkey, value -> - ungrouped_params.put(innerkey, value) - } - params_map.put("Other parameters", ungrouped_params) - - return params_map - } - - // - // Get maximum number of characters across all parameter names - // - private static Integer paramsMaxChars(params_map) { - Integer max_chars = 0 - for (group in params_map.keySet()) { - def group_params = params_map.get(group) // This gets the parameters of that particular group - for (param in group_params.keySet()) { - if (param.size() > max_chars) { - max_chars = param.size() - } - } - } - return max_chars - } -} diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 25a0a74a..408951ae 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -128,7 +128,7 @@ class NfcoreTemplate { def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] def sf = new File("$projectDir/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy index 7674aa79..a8a3d0dc 100755 --- a/lib/WorkflowMain.groovy +++ b/lib/WorkflowMain.groovy @@ -20,40 +20,11 @@ class WorkflowMain { " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } - // - // Generate help string - // - public static String help(workflow, params) { - def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" - def help_string = '' - help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) - help_string += NfcoreSchema.paramsHelp(workflow, params, command) - help_string += '\n' + citation(workflow) + '\n' - help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) - return help_string - } - - // - // Generate parameter summary log string - // - public static String paramsSummaryLog(workflow, params) { - def summary_log = '' - summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) - summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) - summary_log += '\n' + citation(workflow) + '\n' - summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) - return summary_log - } // // Validate parameters and print summary to screen // public static void initialise(workflow, params, log) { - // Print help to screen if required - if (params.help) { - log.info help(workflow, params) - System.exit(0) - } // Print workflow version and exit on --version if (params.version) { @@ -62,14 +33,6 @@ class WorkflowMain { System.exit(0) } - // Print parameter summary log to screen - log.info paramsSummaryLog(workflow, params) - - // Validate workflow parameters via the JSON schema - if (params.validate_params) { - NfcoreSchema.validateParameters(workflow, params, log) - } - // Check that a -profile or Nextflow config has been provided to run the pipeline NfcoreTemplate.checkConfigProvided(workflow, log) diff --git a/lib/WorkflowRnafusion.groovy b/lib/WorkflowRnafusion.groovy index 9c2e78c1..0654f5fc 100755 --- a/lib/WorkflowRnafusion.groovy +++ b/lib/WorkflowRnafusion.groovy @@ -11,6 +11,7 @@ class WorkflowRnafusion { // Check and validate parameters // public static void initialise(params, log) { + genomeExistsError(params, log) @@ -46,15 +47,57 @@ class WorkflowRnafusion { return yaml_file_text } - public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { + // + // Generate methods description for MultiQC + // + + public static String toolCitationText(params) { + + // TODO Optionally add in-text citation tools to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def citation_text = [ + "Tools used in the workflow included:", + "FastQC (Andrews 2010),", + "MultiQC (Ewels et al. 2016)", + "." + ].join(' ').trim() + + return citation_text + } + + public static String toolBibliographyText(params) { + + // TODO Optionally add bibliographic entries to this list. + // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "

  • Author (2023) Pub name, Journal, DOI
    • " : "", + // Uncomment function in methodsDescriptionText to render in MultiQC report + def reference_text = [ + "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + ].join(' ').trim() + + return reference_text + } + + public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) { // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = run_workflow.toMap() meta["manifest_map"] = run_workflow.manifest.toMap() + // Pipeline DOI meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " + // Tool references + meta["tool_citations"] = "" + meta["tool_bibliography"] = "" + + // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! + //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + //meta["tool_bibliography"] = toolBibliographyText(params) + + def methods_text = mqc_methods_yaml.text def engine = new SimpleTemplateEngine() diff --git a/main.nf b/main.nf index b2c34856..af935a03 100644 --- a/main.nf +++ b/main.nf @@ -25,6 +25,22 @@ params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ +include { validateParameters; paramsHelp } from 'plugin/nf-validation' + +// Print help message if needed +if (params.help) { + def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) + def citation = '\n' + WorkflowMain.citation(workflow) + '\n' + def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" + log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs) + System.exit(0) +} + +// Validate input parameters +if (params.validate_params) { + validateParameters() +} + WorkflowMain.initialise(workflow, params, log) /* diff --git a/nextflow.config b/nextflow.config index 1becd30e..2c39b442 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,12 +12,12 @@ params { // TODO nf-core: Specify your pipeline's command line flags // Input options input = null - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false + + // MultiQC options multiqc_config = null multiqc_title = null @@ -27,7 +27,6 @@ params { // Boilerplate options outdir = null - tracedir = "${params.outdir}/pipeline_info" publish_dir_mode = 'copy' email = null email_on_fail = null @@ -36,19 +35,15 @@ params { hook_url = null help = false version = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - // Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null config_profile_contact = null config_profile_url = null - config_profile_name = null - + // Max resource options // Defaults only, expecting to be overwritten @@ -56,6 +51,13 @@ params { max_cpus = 16 max_time = '240.h' + // Schema validation default options + validationFailUnrecognisedParams = false + validationLenientMode = false + validationSchemaIgnoreParams = 'genomes' + validationShowHiddenParams = false + validate_params = true + } // Load base.config by default for all pipelines @@ -75,13 +77,11 @@ try { // } catch (Exception e) { // System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") // } - - profiles { debug { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' - cleanup = false + cleanup = false } conda { conda.enabled = true @@ -104,7 +104,6 @@ profiles { } docker { docker.enabled = true - docker.registry = 'quay.io' docker.userEmulation = true conda.enabled = false singularity.enabled = false @@ -128,7 +127,6 @@ profiles { } podman { podman.enabled = true - podman.registry = 'quay.io' conda.enabled = false docker.enabled = false singularity.enabled = false @@ -172,6 +170,18 @@ profiles { test_full { includeConfig 'conf/test_full.config' } } +// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' + +// Nextflow plugins +plugins { + id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} // Load igenomes.config if required if (!params.igenomes_ignore) { @@ -179,8 +189,6 @@ if (!params.igenomes_ignore) { } else { params.genomes = [:] } - - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -198,19 +206,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail'] def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" } report { enabled = true - file = "${params.tracedir}/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" } trace { enabled = true - file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" } dag { enabled = true - file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" } manifest { @@ -219,7 +227,7 @@ manifest { homePage = 'https://github.com/nf-core/rnafusion' description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' - nextflowVersion = '!>=22.10.1' + nextflowVersion = '!>=23.04.0' version = '2.3.4' doi = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 31308425..6a47c09a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -15,9 +15,9 @@ "input": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/csv", "pattern": "^\\S+\\.csv$", - "schema": "assets/schema_input.json", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/rnafusion/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" @@ -57,6 +57,7 @@ "fasta": { "type": "string", "format": "file-path", + "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", @@ -157,7 +158,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", + "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -174,12 +175,14 @@ "type": "boolean", "description": "Display help text.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "version": { "type": "boolean", "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", + "default": false, "hidden": true }, "publish_dir_mode": { @@ -203,6 +206,7 @@ "type": "boolean", "description": "Send plain-text email instead of HTML.", "fa_icon": "fas fa-remove-format", + "default": false, "hidden": true }, "max_multiqc_email_size": { @@ -217,6 +221,7 @@ "type": "boolean", "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", + "default": false, "hidden": true }, "hook_url": { @@ -228,6 +233,7 @@ }, "multiqc_config": { "type": "string", + "format": "file-path", "description": "Custom config file to supply to MultiQC.", "fa_icon": "fas fa-cog", "hidden": true @@ -243,13 +249,6 @@ "description": "Custom MultiQC yaml file containing HTML including a methods description.", "fa_icon": "fas fa-cog" }, - "tracedir": { - "type": "string", - "description": "Directory to keep pipeline Nextflow logs and reports.", - "default": "${params.outdir}/pipeline_info", - "fa_icon": "fas fa-cogs", - "hidden": true - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,12 +256,29 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "show_hidden_params": { + "validationShowHiddenParams": { "type": "boolean", "fa_icon": "far fa-eye-slash", "description": "Show all params when using `--help`", + "default": false, "hidden": true, "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." + }, + "validationFailUnrecognisedParams": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters fails when an unrecognised parameter is found.", + "default": false, + "hidden": true, + "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + }, + "validationLenientMode": { + "type": "boolean", + "fa_icon": "far fa-check-circle", + "description": "Validation of parameters in lenient more.", + "default": false, + "hidden": true, + "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." } } } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 71b63738..1ea5267f 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -1,21 +1,19 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - VALIDATE INPUTS + PRINT PARAMS SUMMARY ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) +include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' -// Validate input parameters -WorkflowRnafusion.initialise(params, log) +def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) +def citation = '\n' + WorkflowMain.citation(workflow) + '\n' +def summary_params = paramsSummaryMap(workflow) -// TODO nf-core: Add all file path parameters for the pipeline to the list below -// Check input path parameters to see if they exist -def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] -for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } +// Print parameter summary log to screen +log.info logo + paramsSummaryLog(workflow) + citation -// Check mandatory parameters -if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } +WorkflowRnafusion.initialise(params, log) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -69,9 +67,12 @@ workflow RNAFUSION { // SUBWORKFLOW: Read in samplesheet, validate and stage input files // INPUT_CHECK ( - ch_input + file(params.input) ) ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) + // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") + // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ + // ! There is currently no tooling to help you write a sample sheet schema // // MODULE: Run FastQC @@ -91,7 +92,7 @@ workflow RNAFUSION { workflow_summary = WorkflowRnafusion.paramsSummaryMultiqc(workflow, summary_params) ch_workflow_summary = Channel.value(workflow_summary) - methods_description = WorkflowRnafusion.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) + methods_description = WorkflowRnafusion.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params) ch_methods_description = Channel.value(methods_description) ch_multiqc_files = Channel.empty() From 5aa1731651aed47505385f5cb57e343e7da1a269 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 18 Aug 2023 11:35:50 +0200 Subject: [PATCH 003/264] merging template 2.9 --- nextflow.config | 5 ----- 1 file changed, 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 3f1432be..69f5b11c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -301,13 +301,8 @@ manifest { homePage = 'https://github.com/nf-core/rnafusion' description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' -<<<<<<< HEAD nextflowVersion = '!>=23.04.0' version = '2.3.4' -======= - nextflowVersion = '!>=22.10.1' - version = '2.3.4' ->>>>>>> dev doi = '' } From 5778ee63371fc52d17e3c70cdaf960f7fdaee97e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 18 Aug 2023 11:48:20 +0200 Subject: [PATCH 004/264] update modules --- assets/methods_description_template.yml | 5 --- modules.json | 42 +++++++++---------- modules/nf-core/arriba/main.nf | 2 +- modules/nf-core/cat/cat/main.nf | 2 +- modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/cat/fastq/meta.yml | 3 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastp/main.nf | 6 +-- modules/nf-core/fastqc/main.nf | 8 +++- .../nf-core/gatk4/bedtointervallist/main.nf | 14 +++---- .../nf-core/gatk4/bedtointervallist/meta.yml | 7 ++++ .../gatk4/createsequencedictionary/main.nf | 18 ++++---- .../gatk4/createsequencedictionary/meta.yml | 7 ++++ modules/nf-core/kallisto/index/main.nf | 2 +- modules/nf-core/multiqc/main.nf | 6 +-- .../nf-core/picard/collectwgsmetrics/main.nf | 10 ++--- .../nf-core/picard/collectwgsmetrics/meta.yml | 3 +- modules/nf-core/picard/markduplicates/main.nf | 12 +++--- .../nf-core/picard/markduplicates/meta.yml | 11 +++++ modules/nf-core/qualimap/rnaseq/main.nf | 6 +-- modules/nf-core/samtools/faidx/main.nf | 22 ++++++---- modules/nf-core/samtools/faidx/meta.yml | 14 ++++++- modules/nf-core/samtools/index/main.nf | 6 +-- modules/nf-core/samtools/sort/main.nf | 14 +++++-- modules/nf-core/samtools/view/main.nf | 8 ++-- modules/nf-core/samtools/view/meta.yml | 15 ++++--- modules/nf-core/star/align/main.nf | 24 ++++++++--- modules/nf-core/star/align/meta.yml | 8 ++++ modules/nf-core/star/genomegenerate/main.nf | 2 +- modules/nf-core/stringtie/merge/main.nf | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 2 +- 31 files changed, 179 insertions(+), 106 deletions(-) diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 0789eeb1..80452425 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,11 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/rnafusion Methods Description" section_href: "https://github.com/nf-core/rnafusion" plot_type: "html" -<<<<<<< HEAD -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object -======= ->>>>>>> dev data: |

    Methods

    Data was processed using nf-core/rnafusion v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

    diff --git a/modules.json b/modules.json index 78b30658..db763f95 100644 --- a/modules.json +++ b/modules.json @@ -7,107 +7,107 @@ "nf-core": { "arriba": { "branch": "master", - "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cat/cat": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "b6d4d476aee074311c89d82a69c1921bd70c8180", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "20a508676f40d0fd3f911ac595af91ec845704c4", + "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", "installed_by": ["modules"] }, "kallisto/index": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba", + "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", - "git_sha": "2f88b26e9804b99e98f7cd08e74c3f88288a3358", + "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", "installed_by": ["modules"] }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", "installed_by": ["modules"] }, "samtools/view": { "branch": "master", - "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b", + "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f", "installed_by": ["modules"] }, "star/align": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "57d75dbac06812c59798a48585032f6e50bb1914", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", "installed_by": ["modules"] }, "stringtie/merge": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", + "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", "installed_by": ["modules"] } } diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index e4b48be2..a04fe3b7 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -5,7 +5,7 @@ process ARRIBA { conda "bioconda::arriba=2.3.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : - 'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }" + 'biocontainers/arriba:2.3.0--haa8aa89_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 840af4b9..9f062219 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -5,7 +5,7 @@ process CAT_CAT { conda "conda-forge::pigz=2.3.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : - 'quay.io/biocontainers/pigz:2.3.4' }" + 'biocontainers/pigz:2.3.4' }" input: tuple val(meta), path(files_in) diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 8a0b5600..5021e6fc 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -5,7 +5,7 @@ process CAT_FASTQ { conda "conda-forge::sed=4.7" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'ubuntu:20.04' }" + 'nf-core/ubuntu:20.04' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index c836598e..8a39e309 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -1,6 +1,7 @@ name: cat_fastq description: Concatenates fastq files keywords: + - cat - fastq - concatenate tools: @@ -16,7 +17,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: - type: list + type: file description: | List of input FastQ files to be concatenated. output: diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index 800a6099..ebc87273 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -5,7 +5,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { conda "bioconda::multiqc=1.14" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 5eeb9b09..831b7f12 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,10 +2,10 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda "bioconda::fastp=0.23.2" + conda "bioconda::fastp=0.23.4" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' : - 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }" + 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : + 'biocontainers/fastp:0.23.4--h5f740d0_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 9ae58381..249f9064 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -5,7 +5,7 @@ process FASTQC { conda "bioconda::fastqc=0.11.9" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'quay.io/biocontainers/fastqc:0.11.9--0' }" + 'biocontainers/fastqc:0.11.9--0' }" input: tuple val(meta), path(reads) @@ -29,7 +29,11 @@ process FASTQC { printf "%s %s\\n" $rename_to | while read old_name new_name; do [ -f "\${new_name}" ] || ln -s \$old_name \$new_name done - fastqc $args --threads $task.cpus $renamed_files + + fastqc \\ + $args \\ + --threads $task.cpus \\ + $renamed_files cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 41fab003..a23abd06 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -2,14 +2,14 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: tuple val(meta), path(bed) - path dict + tuple val(meta2), path(dict) output: tuple val(meta), path('*.interval_list'), emit: interval_list @@ -22,14 +22,14 @@ process GATK4_BEDTOINTERVALLIST { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" BedToIntervalList \\ + gatk --java-options "-Xmx${avail_mem}M" BedToIntervalList \\ --INPUT $bed \\ --OUTPUT ${prefix}.interval_list \\ --SEQUENCE_DICTIONARY $dict \\ diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 986f1592..40daf752 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -3,6 +3,7 @@ description: Creates an interval list from a bed file and a reference dict keywords: - bed - interval list + - bedtointervallist tools: - gatk4: description: | @@ -23,6 +24,11 @@ input: type: file description: Input bed file pattern: "*.bed" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - dict: type: file description: Sequence dictionary @@ -38,3 +44,4 @@ output: pattern: "versions.yml" authors: - "@kevinmenden" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index bc324ada..15a86bea 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,17 +2,17 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda "bioconda::gatk4=4.3.0.0" + conda "bioconda::gatk4=4.4.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.3.0.0--py36hdfd78af_0': - 'quay.io/biocontainers/gatk4:4.3.0.0--py36hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" input: - path fasta + tuple val(meta), path(fasta) output: - path "*.dict" , emit: dict - path "versions.yml" , emit: versions + tuple val(meta), path('*.dict') , emit: dict + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,14 +20,14 @@ process GATK4_CREATESEQUENCEDICTIONARY { script: def args = task.ext.args ?: '' - def avail_mem = 6 + def avail_mem = 6144 if (!task.memory) { log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" CreateSequenceDictionary \\ + gatk --java-options "-Xmx${avail_mem}M" CreateSequenceDictionary \\ --REFERENCE $fasta \\ --URI $fasta \\ --TMP_DIR . \\ diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 69c23581..a421e681 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -3,6 +3,7 @@ description: Creates a sequence dictionary for a reference sequence keywords: - dictionary - fasta + - createsequencedictionary tools: - gatk: description: | @@ -15,6 +16,11 @@ tools: licence: ["Apache-2.0"] input: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: type: file description: Input fasta file @@ -30,3 +36,4 @@ output: pattern: "versions.yml" authors: - "@maxulysse" + - "@ramprasadn" diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index a24024b4..c866c2a1 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -5,7 +5,7 @@ process KALLISTO_INDEX { conda "bioconda::kallisto=0.46.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - 'quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1' }" + 'biocontainers/kallisto:0.46.2--h4f7b962_1' }" input: path fasta diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 4b604749..65d7dd0d 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 827dfb23..1d59334c 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -5,12 +5,12 @@ process PICARD_COLLECTWGSMETRICS { conda "bioconda::picard=3.0.0 r::r-base" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'quay.io/biocontainers/picard:3.0.0--hdfd78af_1' }" + 'biocontainers/picard:3.0.0--hdfd78af_1' }" input: tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) - tuple val(meta2), path(fai) + tuple val(meta3), path(fai) path intervallist output: @@ -23,16 +23,16 @@ process PICARD_COLLECTWGSMETRICS { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 def interval = intervallist ? "--INTERVALS ${intervallist}" : '' if (!task.memory) { log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ picard \\ - -Xmx${avail_mem}g \\ + -Xmx${avail_mem}M \\ CollectWgsMetrics \\ $args \\ --INPUT $bam \\ diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index 2f8dbd3c..19906f08 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -37,7 +37,7 @@ input: type: file description: Genome fasta file pattern: "*.{fa,fasta,fna}" - - meta2: + - meta3: type: map description: | Groovy Map containing reference information @@ -67,3 +67,4 @@ authors: - "@drpatelh" - "@flowuenne" - "@lassefolkersen" + - "@ramprasadn" diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index be243a95..facd7efb 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -5,12 +5,12 @@ process PICARD_MARKDUPLICATES { conda "bioconda::picard=3.0.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'quay.io/biocontainers/picard:3.0.0--hdfd78af_1' }" + 'biocontainers/picard:3.0.0--hdfd78af_1' }" input: tuple val(meta), path(bam) - path fasta - path fai + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) output: tuple val(meta), path("*.bam") , emit: bam @@ -24,15 +24,15 @@ process PICARD_MARKDUPLICATES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3 + def avail_mem = 3072 if (!task.memory) { log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' } else { - avail_mem = task.memory.giga + avail_mem = (task.memory.mega*0.8).intValue() } """ picard \\ - -Xmx${avail_mem}g \\ + -Xmx${avail_mem}M \\ MarkDuplicates \\ $args \\ --INPUT $bam \\ diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 3f2357bb..f7693d2f 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -25,10 +25,20 @@ input: type: file description: BAM file pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fasta: type: file description: Reference genome fasta file pattern: "*.{fasta,fa}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] - fai: type: file description: Reference genome fasta index @@ -58,3 +68,4 @@ output: authors: - "@drpatelh" - "@projectoriented" + - "@ramprasadn" diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index ad15ebc2..2c0e4105 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -5,7 +5,7 @@ process QUALIMAP_RNASEQ { conda "bioconda::qualimap=2.2.2d" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - 'quay.io/biocontainers/qualimap:2.2.2d--1' }" + 'biocontainers/qualimap:2.2.2d--1' }" input: tuple val(meta), path(bam) @@ -22,7 +22,7 @@ process QUALIMAP_RNASEQ { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" def paired_end = meta.single_end ? '' : '-pe' - def memory = task.memory.toGiga() + "G" + def memory = (task.memory.mega*0.8).intValue() + 'M' def strandedness = 'non-strand-specific' if (meta.strandedness == 'forward') { @@ -32,7 +32,7 @@ process QUALIMAP_RNASEQ { } """ unset DISPLAY - mkdir tmp + mkdir -p tmp export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp qualimap \\ --java-mem-size=$memory \\ diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index ce6580d2..59ed3088 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,18 +2,20 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(fasta) + tuple val(meta2), path(fai) output: - tuple val(meta), path ("*.fai"), emit: fai - tuple val(meta), path ("*.gzi"), emit: gzi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path ("*.{fa,fasta}") , emit: fa , optional: true + tuple val(meta), path ("*.fai") , emit: fai, optional: true + tuple val(meta), path ("*.gzi") , emit: gzi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -23,8 +25,8 @@ process SAMTOOLS_FAIDX { """ samtools \\ faidx \\ - $args \\ - $fasta + $fasta \\ + $args cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -33,8 +35,12 @@ process SAMTOOLS_FAIDX { """ stub: + def match = (task.ext.args =~ /-o(?:utput)?\s(.*)\s?/).findAll() + def fastacmd = match[0] ? "touch ${match[0][1]}" : '' """ + ${fastacmd} touch ${fasta}.fai + cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index fe2fe9a1..957b25e5 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -3,6 +3,7 @@ description: Index FASTA file keywords: - index - fasta + - faidx tools: - samtools: description: | @@ -17,12 +18,21 @@ input: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: type: file description: FASTA file pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - meta: type: map diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 8b95687a..0b20aa4b 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 84c167cd..2b7753fd 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(bam) @@ -23,7 +23,13 @@ process SAMTOOLS_SORT { def prefix = task.ext.prefix ?: "${meta.id}" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam + samtools sort \\ + $args \\ + -@ $task.cpus \\ + -o ${prefix}.bam \\ + -T $prefix \\ + $bam + cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index 729c85e5..cb91facf 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,14 +2,14 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.16.1" + conda "bioconda::samtools=1.17" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' : - 'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : + 'biocontainers/samtools:1.17--h00cdaf9_0' }" input: tuple val(meta), path(input), path(index) - path fasta + tuple val(meta2), path(fasta) path qname output: diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 2e597d34..3b05450b 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -26,12 +26,17 @@ input: description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - index: - type: optional file - description: BAM.BAI/CRAM.CRAI file - pattern: "*.{.bai,.crai}" + type: file + description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) + pattern: "*.{.bai,.csi,.crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: - type: optional file - description: Reference file the CRAM was created with + type: file + description: Reference file the CRAM was created with (optional) pattern: "*.{fasta,fa}" - qname: type: file diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 0e3bd713..8cb8e9a4 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -5,10 +5,10 @@ process STAR_ALIGN { conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads, stageAs: "input*/*") path index path gtf val star_ignore_sjdbgtf @@ -16,19 +16,23 @@ process STAR_ALIGN { val seq_center output: - tuple val(meta), path('*d.out.bam') , emit: bam tuple val(meta), path('*Log.final.out') , emit: log_final tuple val(meta), path('*Log.out') , emit: log_out tuple val(meta), path('*Log.progress.out'), emit: log_progress path "versions.yml" , emit: versions + tuple val(meta), path('*d.out.bam') , optional:true, emit: bam tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq tuple val(meta), path('*.tab') , optional:true, emit: tab + tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab + tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab tuple val(meta), path('*.out.junction') , optional:true, emit: junction tuple val(meta), path('*.out.sam') , optional:true, emit: sam + tuple val(meta), path('*.wig') , optional:true, emit: wig + tuple val(meta), path('*.bg') , optional:true, emit: bedgraph when: task.ext.when == null || task.ext.when @@ -36,20 +40,23 @@ process STAR_ALIGN { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def reads1 = [], reads2 = [] + meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" - def seq_center = seq_center ? "--outSAMattrRGline ID:$prefix 'CN:$seq_center' 'SM:$prefix' $seq_platform " : "--outSAMattrRGline ID:$prefix 'SM:$prefix' $seq_platform " + def seq_center = seq_center ? "'CN:$seq_center'" : "" + def attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ STAR \\ --genomeDir $index \\ - --readFilesIn $reads \\ + --readFilesIn ${reads1.join(",")} ${reads2.join(",")} \\ --runThreadN $task.cpus \\ --outFileNamePrefix $prefix. \\ $out_sam_type \\ $ignore_gtf \\ - $seq_center \\ + $attrRG \\ $args $mv_unsorted_bam @@ -81,11 +88,16 @@ process STAR_ALIGN { touch ${prefix}.sortedByCoord.out.bam touch ${prefix}.toTranscriptome.out.bam touch ${prefix}.Aligned.unsort.out.bam + touch ${prefix}.Aligned.sortedByCoord.out.bam touch ${prefix}.unmapped_1.fastq.gz touch ${prefix}.unmapped_2.fastq.gz touch ${prefix}.tab + touch ${prefix}.SJ.out.tab + touch ${prefix}.ReadsPerGene.out.tab touch ${prefix}.Chimeric.out.junction touch ${prefix}.out.sam + touch ${prefix}.Signal.UniqueMultiple.str1.out.wig + touch ${prefix}.Signal.UniqueMultiple.str1.out.bg cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index 7ee10f1c..bce16d36 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -74,6 +74,14 @@ output: type: file description: STAR chimeric junction output file (optional) pattern: "*.out.junction" + - wig: + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" + - bedgraph: + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 91462489..2407d006 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -5,7 +5,7 @@ process STAR_GENOMEGENERATE { conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" input: path fasta diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index f1635afc..12224f78 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -5,7 +5,7 @@ process STRINGTIE_MERGE { conda "bioconda::stringtie=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'biocontainers/stringtie:2.2.1--hecb563c_2' }" input: path stringtie_gtf diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 2d5b035f..d0f8b563 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -5,7 +5,7 @@ process STRINGTIE_STRINGTIE { conda "bioconda::stringtie=2.2.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'biocontainers/stringtie:2.2.1--hecb563c_2' }" input: tuple val(meta), path(bam) From 7e2772d68c1799a5d60de461d7358bf5d82f3b5d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:40:45 +0200 Subject: [PATCH 005/264] version bump --- .github/workflows/awsfulltest.yml | 1 - CHANGELOG.md | 2 +- README.md | 21 --------------------- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 5 files changed, 4 insertions(+), 26 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 8601db99..31c6cd5f 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -272,4 +272,3 @@ jobs: path: | tower_action_*.log tower_action_*.json - diff --git a/CHANGELOG.md b/CHANGELOG.md index e3e00523..17e9561e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.3.4 - [date] +## v2.3.4dev - [date] ## v2.3.0 - [2022/04/24] diff --git a/README.md b/README.md index 9d64ff1e..3f667dea 100644 --- a/README.md +++ b/README.md @@ -95,27 +95,6 @@ In rnafusion the full-sized test includes reference building and fusion detectio > to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) > with `-profile test` before running the workflow on actual data. - - ```console nextflow run nf-core/rnafusion --input samplesheet.csv --outdir --genome GRCh38 --all -profile ``` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d8d63229..e9edbc07 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnafusion-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 69f5b11c..ffbc21db 100644 --- a/nextflow.config +++ b/nextflow.config @@ -302,7 +302,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.4' + version = '2.3.5dev' doi = '' } From ef98ac9a6672b7bf7a5660da8baf6cb95dc4553e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 21 Aug 2023 14:54:57 +0200 Subject: [PATCH 006/264] add meta info to references in modules --- modules/local/arriba/visualisation/main.nf | 2 +- modules/local/fusionreport/detect/main.nf | 2 +- modules/local/picard/collectrnaseqmetrics/main.nf | 4 ++-- modules/local/pizzly/detect/main.nf | 4 ++-- modules/local/squid/annotate/main.nf | 2 +- modules/local/starfusion/build/main.nf | 4 ++-- modules/local/uscs/custom_gtftogenepred/main.nf | 2 +- 7 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/local/arriba/visualisation/main.nf b/modules/local/arriba/visualisation/main.nf index b55666ca..f97344d1 100644 --- a/modules/local/arriba/visualisation/main.nf +++ b/modules/local/arriba/visualisation/main.nf @@ -9,7 +9,7 @@ process ARRIBA_VISUALISATION { input: tuple val(meta), path(bam), path(bai), path(fusions) - path gtf + tuple val(meta2), path(gtf) path protein_domains path cytobands diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 8c35be4a..2d180113 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -9,7 +9,7 @@ process FUSIONREPORT { input: tuple val(meta), path(reads), path(arriba_fusions), path(pizzly_fusions), path(squid_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) - path(fusionreport_ref) + tuple val(meta2), path(fusionreport_ref) output: path "versions.yml" , emit: versions diff --git a/modules/local/picard/collectrnaseqmetrics/main.nf b/modules/local/picard/collectrnaseqmetrics/main.nf index f1b2fff5..5651c6c1 100644 --- a/modules/local/picard/collectrnaseqmetrics/main.nf +++ b/modules/local/picard/collectrnaseqmetrics/main.nf @@ -9,8 +9,8 @@ process PICARD_COLLECTRNASEQMETRICS { input: tuple val(meta), path(bam), path(bai) - path(refflat) - path(rrna_intervals) + tuple val(meta2), path(refflat) + tuple val(meta3), path(rrna_intervals) output: tuple val(meta), path("*rna_metrics.txt") , emit: metrics diff --git a/modules/local/pizzly/detect/main.nf b/modules/local/pizzly/detect/main.nf index 9f10caf8..a610b531 100644 --- a/modules/local/pizzly/detect/main.nf +++ b/modules/local/pizzly/detect/main.nf @@ -9,8 +9,8 @@ process PIZZLY { input: tuple val(meta), path(txt) - path transcript - path gtf + tuple val(meta2), path(transcript) + tuple val(meta3), path(gtf) output: path "versions.yml" , emit: versions diff --git a/modules/local/squid/annotate/main.nf b/modules/local/squid/annotate/main.nf index 19975b00..9b6eebe7 100644 --- a/modules/local/squid/annotate/main.nf +++ b/modules/local/squid/annotate/main.nf @@ -10,7 +10,7 @@ process SQUID_ANNOTATE { input: tuple val(meta), path(txt) - path gtf + tuple val(meta2), path(gtf) output: tuple val(meta), path("*annotated.txt") , emit: fusions_annotated diff --git a/modules/local/starfusion/build/main.nf b/modules/local/starfusion/build/main.nf index da5b0c3b..e2bd7879 100644 --- a/modules/local/starfusion/build/main.nf +++ b/modules/local/starfusion/build/main.nf @@ -5,8 +5,8 @@ process STARFUSION_BUILD { container "docker.io/trinityctat/starfusion:1.12.0" input: - path fasta - path gtf + tuple val(meta), path(fasta) + tuple val(meta2), path(gtf) output: path "*" , emit: reference diff --git a/modules/local/uscs/custom_gtftogenepred/main.nf b/modules/local/uscs/custom_gtftogenepred/main.nf index 46052b5a..78fcbd29 100644 --- a/modules/local/uscs/custom_gtftogenepred/main.nf +++ b/modules/local/uscs/custom_gtftogenepred/main.nf @@ -7,7 +7,7 @@ process GTF_TO_REFFLAT { 'quay.io/biocontainers/ucsc-gtftogenepred:377--ha8a8165_5' }" input: - path gtf + tuple val(meta), path (gtf) output: path('*.refflat'), emit: refflat From 640c12268d51d6c8c773857f0146c8fa1de0c650 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 21 Aug 2023 14:55:59 +0200 Subject: [PATCH 007/264] remove igenome usage --- nextflow.config | 7 ------- 1 file changed, 7 deletions(-) diff --git a/nextflow.config b/nextflow.config index ffbc21db..8874d640 100644 --- a/nextflow.config +++ b/nextflow.config @@ -256,13 +256,6 @@ plugins { id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet } -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} - // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. From dd3772fa22ca90fc599b9e3e2626f579af4df127 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 15:09:48 +0200 Subject: [PATCH 008/264] Add trim tail for reverse reads --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 7b8f2787..c1e552d5 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -61,7 +61,7 @@ process { } withName: FASTP { - ext.args = params.trim_tail ? "--trim_tail1 ${params.trim_tail}" : '' + ext.args = params.trim_tail ? "--trim_tail1 ${params.trim_tail} --trim_tail2 ${params.trim_tail} " : '' } withName: FASTQC { From 5aeb72794ba586ca0b661d36d0302f0a5fc2e7a5 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 15:16:43 +0200 Subject: [PATCH 009/264] update changelog --- CHANGELOG.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ff835124..db8ab10e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,23 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## v2.3.4dev - [2023/08/21] + +### Added + + +### Changed + + +### Fixed + +- Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) + +### Removed + + + ## v2.3.0 = [2022/04/24] ### Added From 96309174d7624bd223292a5a18b6cd505516d059 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 15:24:43 +0200 Subject: [PATCH 010/264] prettier --- CHANGELOG.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index db8ab10e..5fb2fd31 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,23 +3,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - ## v2.3.4dev - [2023/08/21] ### Added - ### Changed - ### Fixed - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) ### Removed - - ## v2.3.0 = [2022/04/24] ### Added From 90c120bfa3911516594431a468a857220da3d0b0 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 15:38:06 +0200 Subject: [PATCH 011/264] optional html for fusionreport --- modules/local/fusionreport/detect/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 8c35be4a..0bdc3af3 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -16,7 +16,7 @@ process FUSIONREPORT { tuple val(meta), path("*fusionreport.tsv") , emit: fusion_list tuple val(meta), path("*fusionreport_filtered.tsv") , emit: fusion_list_filtered tuple val(meta), path("index.html") , emit: report - tuple val(meta), path("*_*.html") , emit: html + tuple val(meta), path("*_*.html") , optional:true, emit: html tuple val(meta), path("*.csv") , optional:true, emit: csv tuple val(meta), path("*.json") , optional:true, emit: json From 88d10519235b16e6cdb7aa53d808b50a59d7c3f3 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 16:11:40 +0200 Subject: [PATCH 012/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5fb2fd31..272202bd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) +- Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380) ### Removed From fbf1c2e6131b8ccf98d6c51bcf290861c6abe89c Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 16:27:38 +0200 Subject: [PATCH 013/264] use institutional configs by default --- nextflow.config | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 0f0bbc88..37cd5c28 100644 --- a/nextflow.config +++ b/nextflow.config @@ -137,11 +137,11 @@ try { // Load nf-core/rnafusion custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/rnafusion.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") -// } +try { + includeConfig "${params.custom_config_base}/pipeline/rnafusion.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") +} profiles { From 4c277ddaea19f4c9e624deb7ee1b402ba705c89c Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Mon, 21 Aug 2023 16:54:50 +0200 Subject: [PATCH 014/264] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5fb2fd31..04b948cc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) + ### Fixed - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) From 98fb0ba55557b09f2a345b45a83da6a59e61907d Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Tue, 22 Aug 2023 10:27:02 +0200 Subject: [PATCH 015/264] make fusioninspector tsv optional --- modules/local/fusioninspector/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf index 6f59a590..3e94d6a5 100644 --- a/modules/local/fusioninspector/main.nf +++ b/modules/local/fusioninspector/main.nf @@ -10,9 +10,9 @@ process FUSIONINSPECTOR { path reference output: - tuple val(meta), path("*FusionInspector.fusions.tsv") , emit: tsv - path "*" , emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*FusionInspector.fusions.tsv") , optional:true, emit: tsv + path "*" , emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From 1db024652e4d810a28f3eaf3fc1a4c590c9d4c38 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Fri, 25 Aug 2023 08:55:33 +0200 Subject: [PATCH 016/264] Revert "make fusioninspector tsv optional" This reverts commit 98fb0ba55557b09f2a345b45a83da6a59e61907d. --- modules/local/fusioninspector/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf index 3e94d6a5..6f59a590 100644 --- a/modules/local/fusioninspector/main.nf +++ b/modules/local/fusioninspector/main.nf @@ -10,9 +10,9 @@ process FUSIONINSPECTOR { path reference output: - tuple val(meta), path("*FusionInspector.fusions.tsv") , optional:true, emit: tsv - path "*" , emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*FusionInspector.fusions.tsv") , emit: tsv + path "*" , emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From dffeb114b7bae86425ea2b69ed0763e745d59d9e Mon Sep 17 00:00:00 2001 From: Ed Stone Date: Fri, 25 Aug 2023 10:24:25 +0000 Subject: [PATCH 017/264] fix for megafusion key error --- bin/megafusion.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bin/megafusion.py b/bin/megafusion.py index 6f27b296..76872b57 100755 --- a/bin/megafusion.py +++ b/bin/megafusion.py @@ -122,6 +122,8 @@ def column_manipulation(df): df["QUAL"] = "." df["FILTER"] = "PASS" df["REF"] = "N" + df["INFO"] = "" + df["Sample"] = "" for index, row in df.iterrows(): # ALT From 4404ca1918f255d4b643b0213118663599ab3c5a Mon Sep 17 00:00:00 2001 From: Ed Stone Date: Fri, 25 Aug 2023 10:39:03 +0000 Subject: [PATCH 018/264] fix to allow other remote URI paths --- workflows/rnafusion.nf | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 45a9e623..510bc778 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -33,8 +33,11 @@ def checkPathParamList = [ for (param in checkPathParamList) if ((param) && !params.build_references) file(param, checkIfExists: true) -if (params.fasta[0,1] == "s3") { - log.info "INFO: s3 path detected, check for absolute path and trailing '/' not performed" +def params_fasta_path_uri = params.fasta =~ /^([a-zA-Z0-9]*):\/\/(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$/ +// check if params.fasta is a remote uri such as s3://, gs:// or dx:// +if (params_fasta_path_uri){ + log.info "INFO: a remote uri path detected, check for absolute path and trailing '/' not performed" + // log.info "INFO: remote uri path detected (e.g. s3), check for absolute path and trailing '/' not performed" } else { for (param in checkPathParamList) if ((param.toString())!= file(param).toString() && !params.build_references) { exit 1, "Problem with ${param}: ABSOLUTE PATHS are required! Check for trailing '/' at the end of paths too." } From 0699dcaa619c70b47ffc3320656374502bea0165 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 14:33:05 +0200 Subject: [PATCH 019/264] update modules --- assets/multiqc_config.yml | 4 +- modules.json | 12 +++--- modules/nf-core/arriba/main.nf | 20 +++++----- modules/nf-core/arriba/meta.yml | 37 +++++++++++++++++++ .../custom/dumpsoftwareversions/main.nf | 6 +-- modules/nf-core/kallisto/index/main.nf | 6 +-- modules/nf-core/kallisto/index/meta.yml | 20 ++++++++-- modules/nf-core/qualimap/rnaseq/main.nf | 2 +- modules/nf-core/star/align/main.nf | 4 +- modules/nf-core/star/align/meta.yml | 24 ++++++++++++ modules/nf-core/star/genomegenerate/main.nf | 8 ++-- modules/nf-core/star/genomegenerate/meta.yml | 15 ++++++++ 12 files changed, 123 insertions(+), 35 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e9edbc07..9b2226f8 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnafusion-methods-description": order: -1000 diff --git a/modules.json b/modules.json index db763f95..38ba9c33 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "arriba": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "ea9e2892a9d12e8769402f12096219942bcf6536", "installed_by": ["modules"] }, "cat/cat": { @@ -22,7 +22,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "fastp": { @@ -47,7 +47,7 @@ }, "kallisto/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "699fa6f3002d922380615f3847198aeb57d8b6a9", "installed_by": ["modules"] }, "multiqc": { @@ -67,7 +67,7 @@ }, "qualimap/rnaseq": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f", "installed_by": ["modules"] }, "samtools/faidx": { @@ -92,12 +92,12 @@ }, "star/align": { "branch": "master", - "git_sha": "57d75dbac06812c59798a48585032f6e50bb1914", + "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", "installed_by": ["modules"] }, "stringtie/merge": { diff --git a/modules/nf-core/arriba/main.nf b/modules/nf-core/arriba/main.nf index a04fe3b7..2537d05b 100644 --- a/modules/nf-core/arriba/main.nf +++ b/modules/nf-core/arriba/main.nf @@ -2,20 +2,20 @@ process ARRIBA { tag "$meta.id" label 'process_medium' - conda "bioconda::arriba=2.3.0" + conda "bioconda::arriba=2.4.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : - 'biocontainers/arriba:2.3.0--haa8aa89_0' }" + 'https://depot.galaxyproject.org/singularity/arriba:2.4.0--h0033a41_2' : + 'biocontainers/arriba:2.4.0--h0033a41_2' }" input: tuple val(meta), path(bam) - path fasta - path gtf - path blacklist - path known_fusions - path structural_variants - path tags - path protein_domains + tuple val(meta2), path(fasta) + tuple val(meta3), path(gtf) + tuple val(meta4), path(blacklist) + tuple val(meta5), path(known_fusions) + tuple val(meta6), path(structural_variants) + tuple val(meta7), path(tags) + tuple val(meta8), path(protein_domains) output: tuple val(meta), path("*.fusions.tsv") , emit: fusions diff --git a/modules/nf-core/arriba/meta.yml b/modules/nf-core/arriba/meta.yml index 119dd912..85b3a30b 100644 --- a/modules/nf-core/arriba/meta.yml +++ b/modules/nf-core/arriba/meta.yml @@ -3,6 +3,8 @@ description: Arriba is a command-line tool for the detection of gene fusions fro keywords: - fusion - arriba + - detection + - RNA-Seq tools: - arriba: description: Fast and accurate gene fusion detection from RNA-Seq data @@ -22,30 +24,65 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: type: file description: Assembly FASTA file pattern: "*.{fasta}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - gtf: type: file description: Annotation GTF file pattern: "*.{gtf}" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - blacklist: type: file description: Blacklist file pattern: "*.{tsv}" + - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - known_fusions: type: file description: Known fusions file pattern: "*.{tsv}" + - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - structural_variants: type: file description: Structural variants file pattern: "*.{tsv}" + - meta7: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - tags: type: file description: Tags file pattern: "*.{tsv}" + - meta8: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - protein_domains: type: file description: Protein domains file diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf index c866c2a1..fb9e44d9 100644 --- a/modules/nf-core/kallisto/index/main.nf +++ b/modules/nf-core/kallisto/index/main.nf @@ -8,11 +8,11 @@ process KALLISTO_INDEX { 'biocontainers/kallisto:0.46.2--h4f7b962_1' }" input: - path fasta + tuple val(meta), path(fasta) output: - path "kallisto" , emit: idx - path "versions.yml" , emit: versions + tuple val(meta), path("kallisto") , emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml index 47f40c9a..05dfa53d 100644 --- a/modules/nf-core/kallisto/index/meta.yml +++ b/modules/nf-core/kallisto/index/meta.yml @@ -1,6 +1,8 @@ name: kallisto_index description: Create kallisto index keywords: + - kallisto + - kallisto/index - index tools: - kallisto: @@ -12,20 +14,30 @@ tools: licence: ["BSD-2-Clause"] input: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - fasta: type: file description: genome fasta file pattern: "*.{fasta}" output: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - index: + type: directory + description: Kallisto genome index + pattern: "*.idx" - versions: type: file description: File containing software versions pattern: "versions.yml" - - idx: - type: index - description: Kallisto genome index - pattern: "*.idx" authors: - "@ggabernet" diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf index 2c0e4105..044c983f 100644 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ b/modules/nf-core/qualimap/rnaseq/main.nf @@ -9,7 +9,7 @@ process QUALIMAP_RNASEQ { input: tuple val(meta), path(bam) - path gtf + tuple val(meta2), path(gtf) output: tuple val(meta), path("${prefix}"), emit: results diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index 8cb8e9a4..d0e20384 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -9,8 +9,8 @@ process STAR_ALIGN { input: tuple val(meta), path(reads, stageAs: "input*/*") - path index - path gtf + tuple val(meta2), path(index) + tuple val(meta3), path(gtf) val star_ignore_sjdbgtf val seq_platform val seq_center diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index bce16d36..3d8fed0c 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -25,10 +25,34 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - index: type: directory description: STAR genome index pattern: "star" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - seq_platform: + type: string + description: Sequencing platform + - seq_center: + type: string + description: Sequencing center + output: - bam: type: file diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 2407d006..43424042 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -8,12 +8,12 @@ process STAR_GENOMEGENERATE { 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" input: - path fasta - path gtf + tuple val(meta), path(fasta) + tuple val(meta2), path(gtf) output: - path "star" , emit: index - path "versions.yml", emit: versions + tuple val(meta), path("star") , emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 8181157a..eba2d9cf 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -15,14 +15,29 @@ tools: doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - fasta: type: file description: Fasta file of the reference genome + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] - gtf: type: file description: GTF file of the reference genome output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - index: type: directory description: Folder containing the star index files From 3d31b2736b252bb2bbd944a32cfb6a83da85e32c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 14:35:21 +0200 Subject: [PATCH 020/264] bump version --- assets/multiqc_config.yml | 4 +- modules/nf-core/qualimap/rnaseq/meta.yml | 52 ++++++++++++++++++++++++ nextflow.config | 2 +- workflows/rnafusion.nf | 38 ++++++++--------- 4 files changed, 71 insertions(+), 25 deletions(-) create mode 100644 modules/nf-core/qualimap/rnaseq/meta.yml diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 9b2226f8..f02eb657 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnafusion-methods-description": order: -1000 diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml new file mode 100644 index 00000000..7738f08d --- /dev/null +++ b/modules/nf-core/qualimap/rnaseq/meta.yml @@ -0,0 +1,52 @@ +name: qualimap_rnaseq +description: Evaluate alignment data +keywords: + - quality control + - qc + - rnaseq +tools: + - qualimap: + description: | + Qualimap 2 is a platform-independent application written in + Java and R that provides both a Graphical User Interface and + a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts. + homepage: http://qualimap.bioinfo.cipf.es/ + documentation: http://qualimap.conesalab.org/doc_html/index.html + doi: 10.1093/bioinformatics/bts503 + licence: ["GPL-2.0-only"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome + pattern: "*.{gtf}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results: + type: directory + description: Qualimap results dir + pattern: "*/*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@FriederikeHanssen" diff --git a/nextflow.config b/nextflow.config index 8874d640..6e990833 100644 --- a/nextflow.config +++ b/nextflow.config @@ -295,7 +295,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.5dev' + version = '2.4.0dev' doi = '' } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 0658e97a..459b5869 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -20,26 +20,26 @@ WorkflowRnafusion.initialise(params, log) if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or was not specified!' } if (params.fusioninspector_only && !params.fusioninspector_fusions) { exit 1, 'Parameter --fusioninspector_fusions PATH_TO_FUSION_LIST expected with parameter --fusioninspector_only'} -ch_chrgtf = params.starfusion_build ? file(params.chrgtf) : file("${params.starfusion_ref}/ref_annot.gtf") -ch_starindex_ref = params.starfusion_build ? params.starindex_ref : "${params.starfusion_ref}/ref_genome.fa.star.idx" -ch_starindex_ensembl_ref = params.starindex_ref -ch_refflat = params.starfusion_build ? file(params.refflat) : "${params.ensembl_ref}/ref_annot.gtf.refflat" -ch_rrna_interval = params.starfusion_build ? file(params.rrna_intervals) : "${params.ensembl_ref}/ref_annot.interval_list" - +ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() +ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() +ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() +ch_refflat = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect() +ch_rrna_interval = params.starfusion_build ? Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect() +ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect() + +ch_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect() +ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() +ch_transcript = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect() +ch_fai = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect() def checkPathParamList = [ params.fasta, params.fai, params.gtf, - ch_chrgtf, params.transcript, - ch_refflat, - ch_rrna_interval ] - -for (param in checkPathParamList) if ((param) && !params.build_references) file(param, checkIfExists: true) -if (params.fasta[0,1] == "s3") { +if (params.fasta == "s3") { log.info "INFO: s3 path detected, check for absolute path and trailing '/' not performed" } else { @@ -47,12 +47,6 @@ else { } if ((params.squid || params.all) && params.ensembl_version != 102) { exit 1, 'Ensembl version is not supported by squid' } -ch_fasta = file(params.fasta) -ch_gtf = file(params.gtf) -ch_transcript = file(params.transcript) -ch_fai = file(params.fai) - - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CONFIG FILES @@ -115,6 +109,9 @@ workflow RNAFUSION { ch_versions = Channel.empty() + + + // // SUBWORKFLOW: Read in samplesheet, validate and stage input files // @@ -137,9 +134,6 @@ workflow RNAFUSION { } .set { ch_fastq } ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) - // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input") - // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/ - // ! There is currently no tooling to help you write a sample sheet schema CAT_FASTQ ( ch_fastq.multiple @@ -223,7 +217,7 @@ workflow RNAFUSION { //Run fusion-report FUSIONREPORT_WORKFLOW ( ch_reads_all, - params.fusionreport_ref, + ch_fusionreport_ref, ARRIBA_WORKFLOW.out.fusions, PIZZLY_WORKFLOW.out.fusions, SQUID_WORKFLOW.out.fusions, From f6105ce9b99866d2328093814784cd1e590a9d41 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 15:55:57 +0200 Subject: [PATCH 021/264] adapt ENSEMBL and building reference workflow with meta info --- modules/local/ensembl/main.nf | 21 ++++++++++++--------- modules/local/pizzly/download/main.nf | 2 +- workflows/build_references.nf | 15 ++++++--------- 3 files changed, 19 insertions(+), 19 deletions(-) diff --git a/modules/local/ensembl/main.nf b/modules/local/ensembl/main.nf index d6d71e6d..4a782c0d 100644 --- a/modules/local/ensembl/main.nf +++ b/modules/local/ensembl/main.nf @@ -9,13 +9,16 @@ process ENSEMBL_DOWNLOAD { input: val ensembl_version + val genome + val meta output: - path "versions.yml" , emit: versions - path "Homo_sapiens.${params.genome}.${ensembl_version}.all.fa" , emit: fasta - path "Homo_sapiens.${params.genome}.${ensembl_version}.gtf" , emit: gtf - path "Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf" , emit: chrgtf - path "Homo_sapiens.${params.genome}.${ensembl_version}.cdna.all.fa.gz", emit: transcript + tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.all.fa") , emit: fasta + tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.gtf") , emit: gtf + tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.chr.gtf") , emit: chrgtf + tuple val(meta), path("Homo_sapiens.${genome}.${ensembl_version}.cdna.all.fa.gz"), emit: transcript + path "versions.yml" , emit: versions + script: """ @@ -40,10 +43,10 @@ process ENSEMBL_DOWNLOAD { stub: """ - touch "Homo_sapiens.${params.genome}.${ensembl_version}.all.fa" - touch "Homo_sapiens.${params.genome}.${ensembl_version}.gtf" - touch "Homo_sapiens.${params.genome}.${ensembl_version}.chr.gtf" - touch "Homo_sapiens.${params.genome}.${ensembl_version}.cdna.all.fa.gz" + touch "Homo_sapiens.${genome}.${ensembl_version}.all.fa" + touch "Homo_sapiens.${genome}.${ensembl_version}.gtf" + touch "Homo_sapiens.${genome}.${ensembl_version}.chr.gtf" + touch "Homo_sapiens.${genome}.${ensembl_version}.cdna.all.fa.gz" cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/pizzly/download/main.nf b/modules/local/pizzly/download/main.nf index 571cd4dc..efaae3aa 100644 --- a/modules/local/pizzly/download/main.nf +++ b/modules/local/pizzly/download/main.nf @@ -8,7 +8,7 @@ process PIZZLY_DOWNLOAD { 'quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1' }" input: - path transcript + tuple val(meta), path(transcript) output: path "versions.yml" , emit: versions diff --git a/workflows/build_references.nf b/workflows/build_references.nf index c43ecc84..6a03edb6 100644 --- a/workflows/build_references.nf +++ b/workflows/build_references.nf @@ -33,18 +33,15 @@ include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/gatk4/bedto workflow BUILD_REFERENCES { - ENSEMBL_DOWNLOAD( params.ensembl_version ) - ENSEMBL_DOWNLOAD.out.fasta - .map { it -> tuple(id:it.baseName, it) } - .set { ch_fasta_w_meta } + def fake_meta = [:] + fake_meta.id = "Homo_sapiens.${params.genome}.${params.ensembl_version}" + ENSEMBL_DOWNLOAD( params.ensembl_version, params.genome, fake_meta ) - SAMTOOLS_FAIDX(ch_fasta_w_meta) + + SAMTOOLS_FAIDX(ENSEMBL_DOWNLOAD.out.fasta, [[],[]]) GATK4_CREATESEQUENCEDICTIONARY(ENSEMBL_DOWNLOAD.out.fasta) - ENSEMBL_DOWNLOAD.out.gtf - .map { it -> tuple(id:it.baseName, it) } - .set { ch_gtf_w_meta } - RRNA_TRANSCRIPTS(ch_gtf_w_meta) + RRNA_TRANSCRIPTS(ENSEMBL_DOWNLOAD.out.gtf) CONVERT2BED(RRNA_TRANSCRIPTS.out.rrna_gtf) GATK4_BEDTOINTERVALLIST(CONVERT2BED.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict) From 03f304cb6b19478c7de8f1d6837e71af43d457e6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 16:02:45 +0200 Subject: [PATCH 022/264] try to make fasta existence check optional --- nextflow_schema.json | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 195ba8d3..1258d5a7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -322,7 +322,6 @@ "fasta": { "type": "string", "format": "file-path", - "exists": true, "mimetype": "text/plain", "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", "description": "Path to FASTA genome file.", From a17881a8b5b10b2b66a828982a12a82a7575e86d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 16:22:35 +0200 Subject: [PATCH 023/264] fix channel for arriba workflow --- modules/local/arriba/visualisation/main.nf | 4 ++-- nextflow.config | 16 +++++++--------- subworkflows/local/arriba_workflow.nf | 5 ++++- subworkflows/local/fusioninspector_workflow.nf | 4 +++- workflows/rnafusion.nf | 14 ++++++++++++-- 5 files changed, 28 insertions(+), 15 deletions(-) diff --git a/modules/local/arriba/visualisation/main.nf b/modules/local/arriba/visualisation/main.nf index f97344d1..5805a904 100644 --- a/modules/local/arriba/visualisation/main.nf +++ b/modules/local/arriba/visualisation/main.nf @@ -10,8 +10,8 @@ process ARRIBA_VISUALISATION { input: tuple val(meta), path(bam), path(bai), path(fusions) tuple val(meta2), path(gtf) - path protein_domains - path cytobands + tuple val(meta3), path(protein_domains) + tuple val(meta4), path(cytobands) output: tuple val(meta), path("*.pdf") , emit: pdf diff --git a/nextflow.config b/nextflow.config index a9743258..37333c8e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -73,7 +73,7 @@ params { arriba_ref_blacklist = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.3.0.tsv.gz" arriba_ref_cytobands = "${params.genomes_base}/arriba/cytobands_hg38_GRCh38_v2.3.0.tsv" arriba_ref_known_fusions = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz" - arriba_ref_protein_domain = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3" + arriba_ref_protein_domains = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3" fusioncatcher_ref = "${params.genomes_base}/fusioncatcher/human_v102" pizzly_ref = "${params.genomes_base}/pizzly/kallisto" squid_ref = "${params.genomes_base}/squid" @@ -140,13 +140,11 @@ try { // Load nf-core/rnafusion custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! - -try { - includeConfig "${params.custom_config_base}/pipeline/rnafusion.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") -} - +// try { +// includeConfig "${params.custom_config_base}/pipeline/rnafusion.config" +// } catch (Exception e) { +// System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") +// } profiles { debug { dumpHashes = true @@ -297,7 +295,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.4.0dev' + version = '2.3.5dev' doi = '' } diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 0712f787..9f770190 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -10,6 +10,9 @@ workflow ARRIBA_WORKFLOW { ch_gtf ch_fasta ch_starindex_ref + ch_arriba_ref_blacklist + ch_arriba_ref_known_fusions + ch_arriba_ref_protein_domains main: ch_versions = Channel.empty() @@ -34,7 +37,7 @@ workflow ARRIBA_WORKFLOW { .map { meta, reads, fusions -> [ meta, fusions ] } ch_arriba_fusion_fail = ch_dummy_file } else { - ARRIBA ( STAR_FOR_ARRIBA.out.bam, ch_fasta, ch_gtf, params.arriba_ref_blacklist, params.arriba_ref_known_fusions, [], [], params.arriba_ref_protein_domain ) + ARRIBA ( STAR_FOR_ARRIBA.out.bam, ch_fasta, ch_gtf, ch_arriba_ref_blacklist, ch_arriba_ref_known_fusions, [[],[]], [[],[]], ch_arriba_ref_protein_domains ) ch_versions = ch_versions.mix(ARRIBA.out.versions) ch_arriba_fusions = ARRIBA.out.fusions diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 388f42a6..3c224689 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -11,6 +11,8 @@ workflow FUSIONINSPECTOR_WORKFLOW { report bam_sorted_indexed ch_gtf + ch_arriba_ref_protein_domains + ch_arriba_ref_cytobands main: ch_versions = Channel.empty() @@ -38,7 +40,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { if ((params.starfusion || params.all || params.stringtie) && !params.fusioninspector_only && !params.skip_vis) { bam_sorted_indexed_fusions = bam_sorted_indexed.join(FUSIONINSPECTOR.out.tsv) - ARRIBA_VISUALISATION(bam_sorted_indexed_fusions, ch_gtf, params.arriba_ref_protein_domain, params.arriba_ref_cytobands) + ARRIBA_VISUALISATION(bam_sorted_indexed_fusions, ch_gtf, ch_arriba_ref_protein_domains, ch_arriba_ref_cytobands) ch_versions = ch_versions.mix(ARRIBA_VISUALISATION.out.versions) } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 459b5869..0b79053f 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -26,6 +26,11 @@ ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[ ch_refflat = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect() ch_rrna_interval = params.starfusion_build ? Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect() ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands).map { it -> [[id:it.Name], it] }.collect() + ch_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect() ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() @@ -164,7 +169,10 @@ workflow RNAFUSION { ch_reads_all, ch_gtf, ch_fasta, - ch_starindex_ensembl_ref + ch_starindex_ensembl_ref, + ch_arriba_ref_blacklist, + ch_arriba_ref_known_fusions, + ch_arriba_ref_protein_domains ) ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions.first().ifEmpty(null)) @@ -234,7 +242,9 @@ workflow RNAFUSION { FUSIONREPORT_WORKFLOW.out.fusion_list_filtered, FUSIONREPORT_WORKFLOW.out.report, STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed, - ch_chrgtf + ch_chrgtf, + ch_arriba_ref_protein_domains, + ch_arriba_ref_cytobands ) ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions.first().ifEmpty(null)) From 092a6bda990fb2aee47ff18cae9cef4ba73e5774 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 16:25:16 +0200 Subject: [PATCH 024/264] small fix --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 1258d5a7..02cd1e27 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -114,7 +114,7 @@ "fa_icon": "far fa-file-code", "description": "Path to arriba reference known fusions" }, - "arriba_ref_protein_domain": { + "arriba_ref_protein_domains": { "type": "string", "fa_icon": "far fa-file-code", "description": "Path to arriba reference protein domain" From cb169f124003b28bcac21ddc8b06ee4f00ab49d5 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 25 Aug 2023 16:55:38 +0200 Subject: [PATCH 025/264] fix version bump --- CHANGELOG.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 054e3409..4f3c8389 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0 dev +## v2.4.0dev ### Added diff --git a/nextflow.config b/nextflow.config index 37333c8e..107eba8a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -295,7 +295,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.3.5dev' + version = '2.4.0dev' doi = '' } From 68a9fe1c3c6a5d0b47d133633b45283a822468a2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 12:48:26 +0200 Subject: [PATCH 026/264] add gene count by default --- conf/modules.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index c1e552d5..901957d9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -352,7 +352,8 @@ process { --alignInsertionFlush Right \ --alignSplicedMateMapLminOverLmate 0 \ --alignSplicedMateMapLmin 30 \ - --chimOutType Junctions' + --chimOutType Junctions \ + --quantMode GeneCounts' } withName: STAR_GENOMEGENERATE { From 0fbdfd125f7c39a443dadab19972b28374ca13d3 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 16:27:04 +0200 Subject: [PATCH 027/264] fix fusionreport issue with MACOXS dir --- modules/local/fusionreport/download/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index 5dca9b2a..c54910a1 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p2.1" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p3" input: val(username) From 39390f1a9204145a73a0475b38610298309bf0d9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 16:36:07 +0200 Subject: [PATCH 028/264] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03e58659..77bafca0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) - Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380) +- Provide gene count file by default when running STAR_FOR_STARFUSION [#370](https://github.com/nf-core/rnafusion/issues/370) +- Fix fusion-report issue with MACOXS directories [#377](https://github.com/nf-core/rnafusion/issues/377) ### Removed From 1c784f8a977c0654a77cc3e9fc0d159897121bc5 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:25:16 +0200 Subject: [PATCH 029/264] remove redundant indexing in starfusion and qc workflows, output bai files in same dir as bam files --- conf/modules.config | 13 ++----------- subworkflows/local/qc_workflow.nf | 10 ++-------- workflows/rnafusion.nf | 2 +- 3 files changed, 5 insertions(+), 20 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 901957d9..4bee29b3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -187,16 +187,7 @@ process { withName: SAMTOOLS_INDEX_FOR_ARRIBA { publishDir = [ - path: { "${params.outdir}/samtools_index_for_arriba" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SAMTOOLS_INDEX_FOR_QC { - ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)} - publishDir = [ - path: { "${params.outdir}/samtools_index_for_qc" }, + path: { "${params.outdir}/star_for_arriba" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] @@ -204,7 +195,7 @@ process { withName: SAMTOOLS_INDEX_FOR_STARFUSION { publishDir = [ - path: { "${params.outdir}/samtools_index_for_starfusion" }, + path: { "${params.outdir}/star_for_starfusion" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index a2a1dec9..aac1a1d7 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -3,13 +3,12 @@ // include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_QC } from '../../modules/nf-core/samtools/index/main' include { PICARD_COLLECTRNASEQMETRICS } from '../../modules/local/picard/collectrnaseqmetrics/main' include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main' workflow QC_WORKFLOW { take: - bam_sorted + ch_bam_sorted_indexed ch_chrgtf ch_refflat ch_fasta @@ -23,12 +22,7 @@ workflow QC_WORKFLOW { ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions) ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results) - SAMTOOLS_INDEX_FOR_QC(bam_sorted) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_QC.out.versions) - - bam_indexed = bam_sorted.join(SAMTOOLS_INDEX_FOR_QC.out.bai) - - PICARD_COLLECTRNASEQMETRICS(bam_indexed, ch_refflat, ch_rrna_interval) + PICARD_COLLECTRNASEQMETRICS(ch_bam_sorted_indexed, ch_refflat, ch_rrna_interval) ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 510bc778..b196d117 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -240,7 +240,7 @@ workflow RNAFUSION { //QC QC_WORKFLOW ( - STARFUSION_WORKFLOW.out.bam_sorted, + STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed, ch_chrgtf, ch_refflat, ch_fasta, From 6c2a58002cb362fd9e9d860bb16da496854b2109 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:28:09 +0200 Subject: [PATCH 030/264] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03e58659..11d7eb1b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) - +- Remove redundant indexing in starfusion and qc workflows +- Output bai files in same directory as bam files [#373](https://github.com/nf-core/rnafusion/issues/373) ### Fixed - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) From cfec4795991e39827def7153a46f614ced72697f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:29:47 +0200 Subject: [PATCH 031/264] prettier --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 11d7eb1b..b0d6c948 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) - Remove redundant indexing in starfusion and qc workflows - Output bai files in same directory as bam files [#373](https://github.com/nf-core/rnafusion/issues/373) + ### Fixed - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) From 1160d70037b6a2827636761afea219ef048a33b4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:32:43 +0200 Subject: [PATCH 032/264] fix channel i/o --- subworkflows/local/qc_workflow.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index aac1a1d7..56e19425 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -18,7 +18,7 @@ workflow QC_WORKFLOW { main: ch_versions = Channel.empty() - QUALIMAP_RNASEQ(bam_sorted, ch_chrgtf) + QUALIMAP_RNASEQ(ch_bam_sorted_indexed, ch_chrgtf) ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions) ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results) @@ -26,7 +26,7 @@ workflow QC_WORKFLOW { ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics) - PICARD_MARKDUPLICATES(bam_sorted, ch_fasta, ch_fai) + PICARD_MARKDUPLICATES(ch_bam_sorted_indexed, ch_fasta, ch_fai) ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics) From 02fe176847cc347e593f00647c784c8db0d09b64 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:39:25 +0200 Subject: [PATCH 033/264] fix channel i/o as bam_sorted is necessary for some PICARD processes --- subworkflows/local/qc_workflow.nf | 5 +++-- subworkflows/local/starfusion_workflow.nf | 5 +++-- workflows/rnafusion.nf | 1 + 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index 56e19425..066cd2cd 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -8,6 +8,7 @@ include { PICARD_MARKDUPLICATES } from '../../modules/nf-co workflow QC_WORKFLOW { take: + ch_bam_sorted ch_bam_sorted_indexed ch_chrgtf ch_refflat @@ -17,7 +18,7 @@ workflow QC_WORKFLOW { main: ch_versions = Channel.empty() - + bam_sorted QUALIMAP_RNASEQ(ch_bam_sorted_indexed, ch_chrgtf) ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions) ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results) @@ -26,7 +27,7 @@ workflow QC_WORKFLOW { ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics) - PICARD_MARKDUPLICATES(ch_bam_sorted_indexed, ch_fasta, ch_fai) + PICARD_MARKDUPLICATES(bam_sorted, ch_fasta, ch_fai) ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics) diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf index 1656ec7a..4120bc79 100644 --- a/subworkflows/local/starfusion_workflow.nf +++ b/subworkflows/local/starfusion_workflow.nf @@ -51,8 +51,9 @@ workflow STARFUSION_WORKFLOW { emit: fusions = ch_starfusion_fusions star_stats = ch_star_stats - bam_sorted = ch_align - versions = ch_versions.ifEmpty(null) + ch_bam_sorted = ch_align ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty(null) + versions = ch_versions.ifEmpty(null) + } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index b196d117..426e6acf 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -240,6 +240,7 @@ workflow RNAFUSION { //QC QC_WORKFLOW ( + STARFUSION_WORKFLOW.out.ch_bam_sorted, STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed, ch_chrgtf, ch_refflat, From f5c0dc9c592d0b372376413d2739d709e5325fd8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:46:12 +0200 Subject: [PATCH 034/264] fix channel i/o --- subworkflows/local/qc_workflow.nf | 4 ++-- workflows/rnafusion.nf | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index 066cd2cd..9a341f2d 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -18,7 +18,7 @@ workflow QC_WORKFLOW { main: ch_versions = Channel.empty() - bam_sorted + QUALIMAP_RNASEQ(ch_bam_sorted_indexed, ch_chrgtf) ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions) ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results) @@ -27,7 +27,7 @@ workflow QC_WORKFLOW { ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics) - PICARD_MARKDUPLICATES(bam_sorted, ch_fasta, ch_fai) + PICARD_MARKDUPLICATES(ch_bam_sorted, ch_fasta, ch_fai) ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 426e6acf..6612a607 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -207,7 +207,7 @@ workflow RNAFUSION { //Run stringtie STRINGTIE_WORKFLOW ( - STARFUSION_WORKFLOW.out.bam_sorted, + STARFUSION_WORKFLOW.out.ch_bam_sorted, ch_chrgtf ) ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions.first().ifEmpty(null)) From 22c58623c39fb5ca4a878085d2f462974e8fffc5 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 18:23:21 +0200 Subject: [PATCH 035/264] fix channel i/o --- subworkflows/local/qc_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index 9a341f2d..bdf887d1 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -19,7 +19,7 @@ workflow QC_WORKFLOW { main: ch_versions = Channel.empty() - QUALIMAP_RNASEQ(ch_bam_sorted_indexed, ch_chrgtf) + QUALIMAP_RNASEQ(ch_bam_sorted, ch_chrgtf) ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions) ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results) From 74e94ea6bc044f4e7bccf4d5fbeb419967c79d9d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 28 Aug 2023 22:06:56 +0200 Subject: [PATCH 036/264] fix channel i/o for empty channels --- subworkflows/local/starfusion_workflow.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf index 4120bc79..c9ba4bf3 100644 --- a/subworkflows/local/starfusion_workflow.nf +++ b/subworkflows/local/starfusion_workflow.nf @@ -51,8 +51,8 @@ workflow STARFUSION_WORKFLOW { emit: fusions = ch_starfusion_fusions star_stats = ch_star_stats - ch_bam_sorted = ch_align - ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty(null) + ch_bam_sorted = ch_align.ifEmpty([[],[]]) + ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty([[],[],[]]) versions = ch_versions.ifEmpty(null) } From 0bc1378f25b30a6c287fa20bd99587efac12e608 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:20:04 +0200 Subject: [PATCH 037/264] link PR instead of issue --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b0d6c948..0fe75721 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,8 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) -- Remove redundant indexing in starfusion and qc workflows -- Output bai files in same directory as bam files [#373](https://github.com/nf-core/rnafusion/issues/373) +- Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387) +- Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387) ### Fixed From ea8d9eca51b6bac0d141702be364d8d1a74f290e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 30 Aug 2023 10:35:08 +0200 Subject: [PATCH 038/264] update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 77bafca0..a24b1262 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,8 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Tail trimming for reverse reads [#379](https://github.com/nf-core/rnafusion/pull/379) - Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380) -- Provide gene count file by default when running STAR_FOR_STARFUSION [#370](https://github.com/nf-core/rnafusion/issues/370) -- Fix fusion-report issue with MACOXS directories [#377](https://github.com/nf-core/rnafusion/issues/377) +- Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385) +- Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386) ### Removed From ca52d587fea08aaf311d594fac85134e614e1310 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 30 Aug 2023 15:35:19 +0200 Subject: [PATCH 039/264] add branch in case of no fusions --- subworkflows/local/fusioninspector_workflow.nf | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 388f42a6..3602645f 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -15,19 +15,23 @@ workflow FUSIONINSPECTOR_WORKFLOW { main: ch_versions = Channel.empty() index ="${params.starfusion_ref}" - ch_fusion_list = params.fusioninspector_filter ? fusion_list_filtered : fusion_list + ch_fusion_list = ( params.fusioninspector_filter ? fusion_list_filtered : fusion_list ) + .branch{ + no_fusions: it[1].size() == 0 + fusions: it[1].size() > 0 + } if (params.whitelist) { - ch_whitelist = ch_fusion_list.combine(Channel.value(file(params.whitelist, checkIfExists:true))) + ch_whitelist = ch_fusion_list.fusions.combine(Channel.value(file(params.whitelist, checkIfExists:true))) .map { meta, fusions, whitelist -> [ meta, [fusions, whitelist] ] } CAT_CAT(ch_whitelist) // fusioninspector takes care of possible duplicates ch_versions = ch_versions.mix(CAT_CAT.out.versions) - ch_fusion_list = CAT_CAT.out.file_out + ch_fusion_list.fusions = CAT_CAT.out.file_out } - reads_fusion = reads.join(ch_fusion_list ) + reads_fusion = reads.join(ch_fusion_list.fusions ) FUSIONINSPECTOR( reads_fusion, index) ch_versions = ch_versions.mix(FUSIONINSPECTOR.out.versions) From 6966552a235813dd4c898dc41e72f6e0b5ceb19d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 1 Sep 2023 16:10:18 +0200 Subject: [PATCH 040/264] remove check for filter in favor of direct use of tools_cutoff parameter --- conf/modules.config | 1 - modules/local/fusionreport/detect/main.nf | 3 ++- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4bee29b3..b5ba9bdc 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -99,7 +99,6 @@ process { withName: FUSIONREPORT { ext.when = { !params.skip_vis } ext.args = "--export csv" - ext.args2 = { params.fusionreport_filter ? "--tool-cutoff 2" : "--tool-cutoff 1"} publishDir = [ path: { "${params.outdir}/fusionreport/${meta.id}" }, mode: params.publish_dir_mode, diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 0b18c34a..7723ecc5 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -10,6 +10,7 @@ process FUSIONREPORT { input: tuple val(meta), path(reads), path(arriba_fusions), path(pizzly_fusions), path(squid_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) tuple val(meta2), path(fusionreport_ref) + val(tools_cutoff) output: path "versions.yml" , emit: versions @@ -33,7 +34,7 @@ process FUSIONREPORT { tools += params.fusioncatcher || params.all ? "--fusioncatcher ${fusioncatcher_fusions} " : '' def prefix = task.ext.prefix ?: "${meta.id}" """ - fusion_report run $meta.id . $fusionreport_ref $tools --allow-multiple-gene-symbols $args $args2 + fusion_report run $meta.id . $fusionreport_ref $tools --allow-multiple-gene-symbols $tools_cutoff $args $args2 mv fusion_list.tsv ${prefix}.fusionreport.tsv mv fusion_list_filtered.tsv ${prefix}.fusionreport_filtered.tsv From 0a574c2f0c2e56244a8b7ceebea44dc125faa48f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 1 Sep 2023 16:11:34 +0200 Subject: [PATCH 041/264] filters -> tools_cutoff, and adapt documentation --- docs/usage.md | 8 ++-- nextflow.config | 3 +- nextflow_schema.json | 46 ++++++++----------- .../local/fusioninspector_workflow.nf | 7 ++- subworkflows/local/fusionreport_workflow.nf | 2 +- 5 files changed, 28 insertions(+), 38 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 48bb9e10..155aa80c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -164,7 +164,7 @@ nextflow run nf-core/rnafusion \ --trim ``` -#### Filter fusions detected by 2 or more tools +#### Filter out fusions detected by less than INT tools ```bash nextflow run nf-core/rnafusion \ @@ -172,12 +172,10 @@ nextflow run nf-core/rnafusion \ --input \ --genomes_base \ --outdir - --fusioninspector_filter - --fusionreport_filter + --tools_cutoff ``` -`--fusioninspector_filter` feed only fusions detected by 2 or more tools to fusioninspector for closer analysis (false by default). -`--fusionreport_filter` displays only fusions detected by 2 or more tools in fusionreport html index (true by default). +`--tools_cutoff INT` will discard fusions detected by less than INT tools both for display in fusionreport html index and to consider in fusioninspector. #### Adding custom fusions to consider as well as the detected set: whitelist diff --git a/nextflow.config b/nextflow.config index 107eba8a..3034c3e3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -32,8 +32,7 @@ params { starfusion_build = true // Filtering - fusioninspector_filter = false - fusionreport_filter = true + tools_cutoff = 1 // Trimming trim = false diff --git a/nextflow_schema.json b/nextflow_schema.json index 02cd1e27..631734b0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -62,6 +62,16 @@ "fa_icon": "far fa-file-code", "description": "Specifies which analysis type for the pipeline - either build references or analyse data" }, + "cosmic_username": { + "type": "string", + "fa_icon": "far fa-file-code", + "description": "COSMIC username" + }, + "cosmic_passwd": { + "type": "string", + "fa_icon": "far fa-file-code", + "description": "COSMIC password" + }, "genomes_base": { "type": "string", "fa_icon": "far fa-file-code", @@ -149,11 +159,6 @@ "fa_icon": "far fa-file-code", "description": "Path to fusioncatcher references" }, - "fusioninspector_filter": { - "type": "boolean", - "fa_icon": "far fa-file-code", - "description": "Feed filtered fusionreport fusions to fusioninspector" - }, "fusioninspector_limitSjdbInsertNsj": { "type": "integer", "fa_icon": "far fa-file-code", @@ -179,12 +184,6 @@ "fa_icon": "far fa-file-code", "description": "Path to fusionreport references" }, - "fusionreport_filter": { - "type": "boolean", - "fa_icon": "far fa-file-code", - "default": true, - "description": "Display fusions identified with 2 tools or more" - }, "pizzly": { "type": "boolean", "fa_icon": "far fa-file-code", @@ -200,6 +199,11 @@ "fa_icon": "far fa-file-code", "description": "Path to pizzly references" }, + "qiagen": { + "type": "boolean", + "fa_icon": "far fa-file-code", + "description": "Use QIAGEN instead of SANGER to download COSMIC database" + }, "squid": { "type": "boolean", "fa_icon": "far fa-file-code", @@ -245,25 +249,15 @@ "fa_icon": "far fa-file-code", "description": "Run stringtie analysis" }, - "whitelist": { - "type": "string", - "fa_icon": "far fa-file-code", - "description": "Path to fusions to add to the input of fusioninspector" - }, - "cosmic_username": { - "type": "string", + "tools_cutoff": { + "type": "integer", "fa_icon": "far fa-file-code", - "description": "COSMIC username" + "description": "Discard fusions identified by less than INT tools" }, - "cosmic_passwd": { + "whitelist": { "type": "string", "fa_icon": "far fa-file-code", - "description": "COSMIC password" - }, - "qiagen": { - "type": "boolean", - "fa_icon": "far fa-file-code", - "description": "Use QIAGEN instead of SANGER to download COSMIC database" + "description": "Path to fusions to add to the input of fusioninspector" } } }, diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 3c224689..2f1de87e 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -17,19 +17,18 @@ workflow FUSIONINSPECTOR_WORKFLOW { main: ch_versions = Channel.empty() index ="${params.starfusion_ref}" - ch_fusion_list = params.fusioninspector_filter ? fusion_list_filtered : fusion_list if (params.whitelist) { - ch_whitelist = ch_fusion_list.combine(Channel.value(file(params.whitelist, checkIfExists:true))) + ch_whitelist = fusion_list_filtered.combine(Channel.value(file(params.whitelist, checkIfExists:true))) .map { meta, fusions, whitelist -> [ meta, [fusions, whitelist] ] } CAT_CAT(ch_whitelist) // fusioninspector takes care of possible duplicates ch_versions = ch_versions.mix(CAT_CAT.out.versions) - ch_fusion_list = CAT_CAT.out.file_out + fusion_list_filtered = CAT_CAT.out.file_out } - reads_fusion = reads.join(ch_fusion_list ) + reads_fusion = reads.join(fusion_list_filtered ) FUSIONINSPECTOR( reads_fusion, index) ch_versions = ch_versions.mix(FUSIONINSPECTOR.out.versions) diff --git a/subworkflows/local/fusionreport_workflow.nf b/subworkflows/local/fusionreport_workflow.nf index 478986a4..c2bcf201 100644 --- a/subworkflows/local/fusionreport_workflow.nf +++ b/subworkflows/local/fusionreport_workflow.nf @@ -23,7 +23,7 @@ workflow FUSIONREPORT_WORKFLOW { .join(starfusion_fusions, remainder: true) .join(fusioncatcher_fusions, remainder: true) - FUSIONREPORT(reads_fusions, fusionreport_ref) + FUSIONREPORT(reads_fusions, fusionreport_ref, params.tools_cutoff) ch_fusion_list = FUSIONREPORT.out.fusion_list ch_fusion_list_filtered = FUSIONREPORT.out.fusion_list_filtered ch_versions = ch_versions.mix(FUSIONREPORT.out.versions) From bec1a763fb74f79ec55517862d8934f43e920ffb Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 1 Sep 2023 18:03:14 +0200 Subject: [PATCH 042/264] add actual argument for tools-cutoff in fusionreport --- modules/local/fusionreport/detect/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 7723ecc5..6b5cbf9c 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -34,7 +34,7 @@ process FUSIONREPORT { tools += params.fusioncatcher || params.all ? "--fusioncatcher ${fusioncatcher_fusions} " : '' def prefix = task.ext.prefix ?: "${meta.id}" """ - fusion_report run $meta.id . $fusionreport_ref $tools --allow-multiple-gene-symbols $tools_cutoff $args $args2 + fusion_report run $meta.id . $fusionreport_ref $tools --allow-multiple-gene-symbols --tool-cutoff $tools_cutoff $args $args2 mv fusion_list.tsv ${prefix}.fusionreport.tsv mv fusion_list_filtered.tsv ${prefix}.fusionreport_filtered.tsv From 961b70dc71706d91e09b8e277bff246b8369eac8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Sep 2023 11:26:23 +0200 Subject: [PATCH 043/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e57f2ea6..a0d38753 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) - Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387) - Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387) +- Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389) ### Fixed From 6b799843239247e48de5539980f9b117b99b35cc Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Sep 2023 12:30:44 +0200 Subject: [PATCH 044/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e57f2ea6..3442440b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380) - Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385) - Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386) +- The fusion lists is updated to contain to branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388) ### Removed From 72ee2ec186eec1e44e03704d66c9ec6314ac149d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 4 Sep 2023 13:26:29 +0200 Subject: [PATCH 045/264] Update CHANGELOG.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3442440b..731dadb7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380) - Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385) - Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386) -- The fusion lists is updated to contain to branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388) +- The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388) ### Removed From 491501c9f6ac97f518ab4a46034581869e8546aa Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 10:43:09 +0200 Subject: [PATCH 046/264] add validation of tools_cutoff values --- workflows/rnafusion.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 1fbaee3e..49e60056 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -19,6 +19,8 @@ WorkflowRnafusion.initialise(params, log) if (file(params.input).exists() || params.build_references) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet does not exist or was not specified!' } if (params.fusioninspector_only && !params.fusioninspector_fusions) { exit 1, 'Parameter --fusioninspector_fusions PATH_TO_FUSION_LIST expected with parameter --fusioninspector_only'} +if (params.tools_cutoff < 1) { exit 1, 'Parameter: --tools_cutoff should be >= 1'} + ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() From 9abda97bd3fe65176a8e2b59c381801a3d280219 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 10:44:22 +0200 Subject: [PATCH 047/264] refactor channel names --- subworkflows/local/fusioninspector_workflow.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 4d60bfae..733858fb 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -34,18 +34,18 @@ workflow FUSIONINSPECTOR_WORKFLOW { ch_fusion_list.fusions = CAT_CAT.out.file_out } - reads_fusion = reads.join(ch_fusion_list.fusions ) + ch_reads_fusion = reads.join(ch_fusion_list.fusions ) - FUSIONINSPECTOR( reads_fusion, index) + FUSIONINSPECTOR( ch_reads_fusion, index) ch_versions = ch_versions.mix(FUSIONINSPECTOR.out.versions) - fusion_data = FUSIONINSPECTOR.out.tsv.join(report) - MEGAFUSION(fusion_data) + ch_fusion_data = FUSIONINSPECTOR.out.tsv.join(report) + MEGAFUSION(ch_fusion_data) ch_versions = ch_versions.mix(MEGAFUSION.out.versions) if ((params.starfusion || params.all || params.stringtie) && !params.fusioninspector_only && !params.skip_vis) { - bam_sorted_indexed_fusions = bam_sorted_indexed.join(FUSIONINSPECTOR.out.tsv) - ARRIBA_VISUALISATION(bam_sorted_indexed_fusions, ch_gtf, ch_arriba_ref_protein_domains, ch_arriba_ref_cytobands) + ch_bam_sorted_indexed_fusions = bam_sorted_indexed.join(FUSIONINSPECTOR.out.tsv) + ARRIBA_VISUALISATION(ch_bam_sorted_indexed_fusions, ch_gtf, ch_arriba_ref_protein_domains, ch_arriba_ref_cytobands) ch_versions = ch_versions.mix(ARRIBA_VISUALISATION.out.versions) } From 96cc533c5fc95baea653499f56f2ce6290eb512c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 13:42:17 +0200 Subject: [PATCH 048/264] remove sorting and indexing of star_for_arriba bam, changing filenames --- conf/modules.config | 5 ++++- subworkflows/local/arriba_workflow.nf | 18 ++++++++---------- 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 4bee29b3..a13d8b10 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -210,7 +210,7 @@ process { } withName: SAMTOOLS_SORT_FOR_ARRIBA { - ext.prefix = { "${meta.id}_sorted" } + ext.prefix = { "${meta.id}_star_for_arriba_sorted" } publishDir = [ path: { "${params.outdir}/samtools_sort_for_arriba" }, mode: params.publish_dir_mode, @@ -229,6 +229,7 @@ process { withName: SAMTOOLS_VIEW_FOR_ARRIBA { ext.args = { "--output-fmt cram" } + ext.prefix = { "${meta.id}_star_for_arriba" } publishDir = [ path: { "${params.outdir}/cram_arriba" }, mode: params.publish_dir_mode, @@ -248,6 +249,7 @@ process { withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM { ext.args = { "--output-fmt cram" } + ext.prefix = { "${meta.id}_star_for_squid_sorted" } publishDir = [ path: { "${params.outdir}/cram_squid" }, mode: params.publish_dir_mode, @@ -267,6 +269,7 @@ process { withName: SAMTOOLS_VIEW_FOR_STARFUSION { ext.args = { "--output-fmt cram" } + ext.prefix = { "${meta.id}_star_for_starfusion_sorted" } publishDir = [ path: { "${params.outdir}/cram_starfusion" }, mode: params.publish_dir_mode, diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 9f770190..114e64ba 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -23,16 +23,7 @@ workflow ARRIBA_WORKFLOW { STAR_FOR_ARRIBA( reads, ch_starindex_ref, ch_gtf, params.star_ignore_sjdbgtf, '', params.seq_center ?: '') ch_versions = ch_versions.mix(STAR_FOR_ARRIBA.out.versions) - SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions) - - SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_ARRIBA.out.versions) - - bam_indexed = SAMTOOLS_SORT_FOR_ARRIBA.out.bam.join(SAMTOOLS_INDEX_FOR_ARRIBA.out.bai) - if (params.arriba_fusions) { - // [meta, reads], fusions -> [meta, fusions] ch_arriba_fusions = reads.combine( Channel.value( file( params.arriba_fusions, checkIfExists: true ) ) ) .map { meta, reads, fusions -> [ meta, fusions ] } ch_arriba_fusion_fail = ch_dummy_file @@ -45,9 +36,16 @@ workflow ARRIBA_WORKFLOW { } if (params.cram.contains('arriba') ){ + // SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam) + // ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions) + + // SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam) + // ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_ARRIBA.out.versions) + + bam_indexed = SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] } + SAMTOOLS_VIEW_FOR_ARRIBA(bam_indexed, ch_fasta, []) ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions ) - } From 2bf946a05344a2e7f1ede4eba374d74cb9bfb945 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 15:46:11 +0200 Subject: [PATCH 049/264] add filename changes --- conf/modules.config | 5 +++-- modules/local/fusionreport/detect/main.nf | 1 + subworkflows/local/arriba_workflow.nf | 9 +-------- 3 files changed, 5 insertions(+), 10 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index a13d8b10..6ff57e26 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -36,7 +36,8 @@ process { } withName: ARRIBA_VISUALISATION { - ext.when = { !params.fusioninspector_only && (params.starfusion || params.all) } + ext.when = { !params.fusioninspector_only && (params.starfusion || params.all) } + ext.prefix = { "${meta.id}_combined_fusions_arriba_visualisation" } publishDir = [ path: { "${params.outdir}/arriba_visualisation" }, mode: params.publish_dir_mode, @@ -269,7 +270,7 @@ process { withName: SAMTOOLS_VIEW_FOR_STARFUSION { ext.args = { "--output-fmt cram" } - ext.prefix = { "${meta.id}_star_for_starfusion_sorted" } + ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" } publishDir = [ path: { "${params.outdir}/cram_starfusion" }, mode: params.publish_dir_mode, diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 0b18c34a..3d5853a7 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -37,6 +37,7 @@ process FUSIONREPORT { mv fusion_list.tsv ${prefix}.fusionreport.tsv mv fusion_list_filtered.tsv ${prefix}.fusionreport_filtered.tsv + mv index.html ${prefix}_fusionreport_index.html [ ! -f fusions.csv ] || mv fusions.csv ${prefix}.fusions.csv [ ! -f fusions.json ] || mv fusions.json ${prefix}.fusions.json diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 114e64ba..3255d6d9 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -36,15 +36,8 @@ workflow ARRIBA_WORKFLOW { } if (params.cram.contains('arriba') ){ - // SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam) - // ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions) - // SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam) - // ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_ARRIBA.out.versions) - - bam_indexed = SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] } - - SAMTOOLS_VIEW_FOR_ARRIBA(bam_indexed, ch_fasta, []) + SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, []) ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions ) } From 00b97e84e72d37677b0e3f6681d18d2223cdf3fa Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 16:47:08 +0200 Subject: [PATCH 050/264] remove trimmed fastqc report from multiqc --- workflows/rnafusion.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 1fbaee3e..6f498e11 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -288,7 +288,6 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_reports.ifEmpty([])) From 08e48316f6707b6661412a274ede2c4eec072e63 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 16:49:02 +0200 Subject: [PATCH 051/264] remove channels needed from the trim workflow to the multiqc report --- subworkflows/local/trim_workflow.nf | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf index 01baeec7..bf3781f8 100644 --- a/subworkflows/local/trim_workflow.nf +++ b/subworkflows/local/trim_workflow.nf @@ -10,7 +10,6 @@ workflow TRIM_WORKFLOW { main: ch_versions = Channel.empty() - ch_reports = Channel.empty() if (params.trim) { @@ -21,7 +20,6 @@ workflow TRIM_WORKFLOW { ch_reads_all = reads ch_reads_fusioncatcher = REFORMAT.out.reads_out - ch_reports = FASTQC_FOR_TRIM.out.zip.collect{it[1]}.ifEmpty([]) } else if (params.fastp_trim) { FASTP(reads, params.adapter_fasta, false, false) @@ -32,11 +30,7 @@ workflow TRIM_WORKFLOW { ch_reads_all = FASTP.out.reads ch_reads_fusioncatcher = ch_reads_all - ch_reports = ch_reports.mix( - FASTQC_FOR_FASTP.out.zip.collect{it[1]}.ifEmpty([]), - FASTP.out.json.collect{meta, json -> json}, - FASTP.out.html.collect{meta, html -> html} - ) + } else { ch_reads_all = reads @@ -46,7 +40,6 @@ workflow TRIM_WORKFLOW { emit: ch_reads_all ch_reads_fusioncatcher - ch_reports versions = ch_versions.ifEmpty(null) } From 7cc05672c4489d4ec2c8d09f395d6d380dacbdfb Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 16:51:27 +0200 Subject: [PATCH 052/264] fix arriba cram from bam used in arriba --- subworkflows/local/arriba_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 3255d6d9..5bbd7ea2 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -37,7 +37,7 @@ workflow ARRIBA_WORKFLOW { if (params.cram.contains('arriba') ){ - SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, []) + SAMTOOLS_VIEW_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, []) ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions ) } From 4ff060eb227e10de39e67f495337138b10f1d4d8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 16:57:50 +0200 Subject: [PATCH 053/264] remove specification for unused modules --- conf/modules.config | 19 +------------------ subworkflows/local/arriba_workflow.nf | 2 -- 2 files changed, 1 insertion(+), 20 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 6ff57e26..29d28a9f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -186,14 +186,6 @@ process { ] } - withName: SAMTOOLS_INDEX_FOR_ARRIBA { - publishDir = [ - path: { "${params.outdir}/star_for_arriba" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: SAMTOOLS_INDEX_FOR_STARFUSION { publishDir = [ path: { "${params.outdir}/star_for_starfusion" }, @@ -202,7 +194,7 @@ process { ] } - withName: SAMTOOLS_FAIDX { + withName: SAMTOOLS_FAIDX { publishDir = [ path: { "${params.genomes_base}/ensembl" }, mode: params.publish_dir_mode, @@ -210,15 +202,6 @@ process { ] } - withName: SAMTOOLS_SORT_FOR_ARRIBA { - ext.prefix = { "${meta.id}_star_for_arriba_sorted" } - publishDir = [ - path: { "${params.outdir}/samtools_sort_for_arriba" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: SAMTOOLS_SORT_FOR_SQUID_CHIMERIC { ext.prefix = { "${meta.id}_chimeric_sorted" } publishDir = [ diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 5bbd7ea2..36c3924f 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -1,6 +1,4 @@ include { ARRIBA } from '../../modules/nf-core/arriba/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_ARRIBA} from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_FOR_ARRIBA } from '../../modules/nf-core/samtools/sort/main' include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_ARRIBA} from '../../modules/nf-core/samtools/view/main' include { STAR_ALIGN as STAR_FOR_ARRIBA } from '../../modules/nf-core/star/align/main' From d61601a53f00b58fad920e8b4c826883601d732d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 6 Sep 2023 16:58:59 +0200 Subject: [PATCH 054/264] change regex to emit fusionreport index --- modules/local/fusionreport/detect/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 3d5853a7..e3ea5149 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -15,7 +15,7 @@ process FUSIONREPORT { path "versions.yml" , emit: versions tuple val(meta), path("*fusionreport.tsv") , emit: fusion_list tuple val(meta), path("*fusionreport_filtered.tsv") , emit: fusion_list_filtered - tuple val(meta), path("index.html") , emit: report + tuple val(meta), path("*index.html") , emit: report tuple val(meta), path("*_*.html") , optional:true, emit: html tuple val(meta), path("*.csv") , optional:true, emit: csv tuple val(meta), path("*.json") , optional:true, emit: json From cae8374a9c5754d21a1fdb542cffded3d728cd12 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:21:10 +0200 Subject: [PATCH 055/264] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e57f2ea6..854e8bba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed +- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394) + ## v2.3.0 = [2022/04/24] ### Added From 060650fc7b442cbe51705102e0a7b5a19f4c1b67 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:31:15 +0200 Subject: [PATCH 056/264] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e57f2ea6..854e8bba 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed +- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394) + ## v2.3.0 = [2022/04/24] ### Added From 9ce149c305c3742029fb2c3f9c265682c36e1461 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:44:54 +0200 Subject: [PATCH 057/264] reverse squid change --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 29d28a9f..911fe292 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -233,7 +233,6 @@ process { withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM { ext.args = { "--output-fmt cram" } - ext.prefix = { "${meta.id}_star_for_squid_sorted" } publishDir = [ path: { "${params.outdir}/cram_squid" }, mode: params.publish_dir_mode, From 57337c237b28f49622e269c8fcf27cb4529d90a4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 8 Sep 2023 10:48:42 +0200 Subject: [PATCH 058/264] update changelog --- CHANGELOG.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 854e8bba..056aa71e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed -- Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394) +- `samtools sort` and `samtools index` for `arriba` workflow were dispensable and were removed [#395](https://github.com/nf-core/rnafusion/pull/395) ## v2.3.0 = [2022/04/24] @@ -39,6 +39,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `Arriba` visualisation now runs for FusionInspector (combined tools) results, not only `Arriba` results - Updated metro map with trimming options and placed `Arriba` visualisation after `FusionInspector` - Exit with error when using squid in combination with any ensembl version different from 102 +- Renaming [#395](https://github.com/nf-core/rnafusion/pull/395) + - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation + - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba + - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out + - `fusion-report` index.html file to meta.id_fusionreport_index.html ### Fixed From 0b02de31fabde245f1c83b9f93e4150cba8d94fc Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 11 Sep 2023 12:18:11 +0200 Subject: [PATCH 059/264] update intro and usage documentation --- README.md | 122 ++++++++++---------- bin/get_rrna_transcripts.py | 1 - docs/usage.md | 223 +++++++++++++++--------------------- 3 files changed, 153 insertions(+), 193 deletions(-) diff --git a/README.md b/README.md index 3f667dea..17559918 100644 --- a/README.md +++ b/README.md @@ -12,24 +12,7 @@ ## Introduction -**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing analysis pipeline with curated list of tools for detecting and visualizing fusion genes. - -The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! - -> **IMPORTANT: conda is not supported currently.** Run with singularity or docker. - -> GRCh38 is the only supported reference - -| Tool | Version | -| --------------------------------------------------------- | :------: | -| [Arriba](https://github.com/suhrig/arriba) | `2.3.0` | -| [FusionCatcher](https://github.com/ndaniel/fusioncatcher) | `1.33` | -| [Pizzly](https://github.com/pmelsted/pizzly) | `0.37.3` | -| [Squid](https://github.com/Kingsford-Group/squid) | `1.5` | -| [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) | `1.10.1` | -| [StringTie](https://github.com/gpertea/stringtie) | `2.2.1` | - -> Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. +**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results). @@ -39,54 +22,52 @@ In rnafusion the full-sized test includes reference building and fusion detectio ![nf-core/rnafusion metro map](docs/images/nf-core-rnafusion_metro_map.png) -#### Build references +### Build references -`--build_references` triggers a parallel workflow to build all references +`--build_references` triggers a parallel workflow to build references, which is a prerequisite to running the pipeline: 1. Download ensembl fasta and gtf files -2. Create STAR index -3. Download arriba references -4. Download fusioncatcher references -5. Download pizzly references (kallisto index) -6. Download and build STAR-fusion references -7. Download fusion-report DBs +2. Create [STAR](https://github.com/alexdobin/STAR) index +3. Download [Arriba](https://github.com/suhrig/arriba) references +4. Download [FusionCatcher](https://github.com/ndaniel/fusioncatcher) references +5. Download [Pizzly](https://github.com/pmelsted/pizzly) references ([kallisto](https://pachterlab.github.io/kallisto/manual) index) +6. Download and build [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) references +7. Download [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) DBs #### Main workflow 1. Input samplesheet check -2. Concatenate fastq files per sample -3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -4. Arriba subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [Samtool](https://github.com/samtools/samtools) sort - - [Samtool](https://github.com/samtools/samtools) index - - [Arriba](https://github.com/suhrig/arriba) fusion detection -5. Pizzly subworkflow - - [Kallisto](https://pachterlab.github.io/kallisto/) quantification - - [Pizzly](https://github.com/pmelsted/pizzly) fusion detection -6. Squid subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [Samtools view](http://www.htslib.org/): convert sam output from STAR to bam - - [Samtools sort](http://www.htslib.org/): bam output from STAR - - [SQUID](https://github.com/Kingsford-Group/squid) fusion detection - - [SQUID](https://github.com/Kingsford-Group/squid) annotate -7. STAR-fusion subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection -8. Fusioncatcher subworkflow - - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection -9. Fusion-report subworkflow - - Merge all fusions detected by the different tools - - [Fusion-report](https://github.com/matq007/fusion-report) -10. FusionInspector subworkflow +2. Concatenate fastq files per sample ([cat](http://www.linfo.org/cat.html)) +3. Reads quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) +4. Optional trimming with [fastp](https://github.com/OpenGene/fastp) +5. Arriba subworkflow + - [STAR](https://github.com/alexdobin/STAR) alignment + - [Arriba](https://github.com/suhrig/arriba) fusion detection +6. Pizzly subworkflow + - [Kallisto](https://pachterlab.github.io/kallisto/) quantification + - [Pizzly](https://github.com/pmelsted/pizzly) fusion detection +7. Squid subworkflow + - [STAR](https://github.com/alexdobin/STAR) alignment + - [Samtools view](http://www.htslib.org/): convert sam output from STAR to bam + - [Samtools sort](http://www.htslib.org/): bam output from STAR + - [SQUID](https://github.com/Kingsford-Group/squid) fusion detection + - [SQUID](https://github.com/Kingsford-Group/squid) annotate +8. STAR-fusion subworkflow + - [STAR](https://github.com/alexdobin/STAR) alignment + - [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection +9. Fusioncatcher subworkflow + - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection +10. StringTie subworkflow + - [StringTie](https://ccb.jhu.edu/software/stringtie/) +11. Fusion-report + - Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) +12. Post-processing and analysis of data - [FusionInspector](https://github.com/FusionInspector/FusionInspector) - [Arriba](https://github.com/suhrig/arriba) visualisation -11. Stringtie subworkflow - - [StringTie](https://ccb.jhu.edu/software/stringtie/index.shtml) -12. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -13. QC for mapped reads ([`QualiMap: BAM QC`](https://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html)) -14. Index mapped reads ([samtools index](http://www.htslib.org/)) -15. Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-) and ([`picard MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-)) + - QC for mapped reads ([`QualiMap: BAM QC`](https://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html)) + - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-) and ([`picard MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-)) +13. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +14. Compress bam files to cram with [samtools view](http://www.htslib.org/) ## Usage @@ -95,23 +76,36 @@ In rnafusion the full-sized test includes reference building and fusion detectio > to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) > with `-profile test` before running the workflow on actual data. -```console -nextflow run nf-core/rnafusion --input samplesheet.csv --outdir --genome GRCh38 --all -profile -``` +As the reference building is computationally heavy (> 24h on HPC), it is recommended to test the pipeline with the `-stub` parameter (creation of empty files): + +First build the references: ```bash -nextflow run nf-core/rnafusion --input samplesheet.csv --outdir --genome GRCh37 -profile +nextflow run nf-core/rnafusion \ + -profile \ + -profile test \ + --outdir \ + --build_references \ + -stub ``` -> Note that paths need to be absolute and that runs with conda are not supported. +Then perform the analysis: ```bash nextflow run nf-core/rnafusion \ -profile \ - --input samplesheet.csv \ - --outdir + -profile test \ + --outdir \ + -stub ``` +> **Notes:** +> +> - conda is not supported currently, run with singularity or docker +> - Paths need to be absolute +> - GRCh38 is the only supported reference +> - Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. + > **Warning:** > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; diff --git a/bin/get_rrna_transcripts.py b/bin/get_rrna_transcripts.py index 46812caf..670d5f06 100755 --- a/bin/get_rrna_transcripts.py +++ b/bin/get_rrna_transcripts.py @@ -8,7 +8,6 @@ def get_rrna_intervals(file_in, file_out): """ - Get the commented out header Get lines containing ``#`` or ``gene_type rRNA`` or ```` or ``gene_type rRNA_pseudogene`` or ``gene_type MT_rRNA`` Create output file diff --git a/docs/usage.md b/docs/usage.md index 48bb9e10..9df6d24e 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -4,31 +4,27 @@ > _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ -## Introduction +## Pipeline summary The pipeline is divided into two parts: 1. Download and build references - specified with `--build_references` parameter - required only once before running the pipeline - - **Important**: rerun with each new release + - **Important**: has to be run with each new release 2. Detecting fusions - - Supported tools: `Arriba`, `FusionCatcher`, `pizzly`, `SQUID`, `STAR-Fusion` and `StringTie` - - QC: `Fastqc` and `MultiQC` - - Fusion visualization: `Arriba` (only fusion detected with Arriba), `fusion-report` and `FusionInspector` + - Supported tools: `Arriba`, `FusionCatcher`, `pizzly`, `SQUID`, `STAR-Fusion`, and `StringTie` + - QC: `Fastqc`, `MultiQC`, and `Qualimap rnaseq` + - Fusions visualization: `Arriba`, `fusion-report` and `FusionInspector`, VCF file creation based on `MegaFusion` -### 1. Download and build references +## Download and build references The rnafusion pipeline needs references for the fusion detection tools, so downloading these is a **requirement**. -Whilst it is possible to download and build each reference manually, it is advised to download references with the rnafusion pipeline. -First register for a free account at COSMIC at [https://cancer.sanger.ac.uk/cosmic/register](https://cancer.sanger.ac.uk/cosmic/register) using your university email. The account is **only activated upon** clicking the link in the registration email. - -Download the references as shown below including your COSMIC credentials. - -> Note that this step takes about 24 hours to complete on HPC. - -> Do not provide a samplesheet via the `input` parameter, otherwise the pipeline will run the analysis directly after downloading the references (except if that is what you want). +> **IMPORTANT** +> +> - Note that this step takes about 24 hours to complete on HPC. +> - Do not provide a samplesheet via the `input` parameter, otherwise the pipeline will run the analysis directly after downloading the references (except if that is what you want). ```bash nextflow run nf-core/rnafusion \ @@ -48,7 +44,15 @@ nextflow run nf-core/rnafusion \ --outdir ``` -#### Using QIAGEN download insead of SANGER (non-academic usage) for the COSMIC database +### Downloading the cosmic database with SANGER or QUIAGEN + +#### For academic users + +First register for a free account at COSMIC at [https://cancer.sanger.ac.uk/cosmic/register](https://cancer.sanger.ac.uk/cosmic/register) using a university email. The account is **only activated upon** clicking the link in the registration email. + +#### For non-academic users + +Use credentials from QIAGEN and add `--qiagen` ```bash nextflow run nf-core/rnafusion \ @@ -58,23 +62,13 @@ nextflow run nf-core/rnafusion \ --outdir --qiagen ``` -#### References directory tree +#### STAR-Fusion references downloaded vs built -```text -references/ -|-- arriba -|-- ensembl -|-- fusion_report_db -|-- fusioncatcher -| `-- human_v102 -|-- pizzly -|-- star -`-- starfusion -``` +By default STAR-Fusion references are **built**. You can also download them from [CTAT](https://github.com/NCIP/Trinity_CTAT/wiki) by using the flag `--starfusion_build FALSE` for both reference building and fusion detection. This allows more flexibility for different organisms but **be aware that STAR-Fusion reference download is not recommended as not fully tested!** #### Issues with building references -If process `FUSIONREPORT_DOWNLOAD` times out, it could be due to network restriction (e.g. if trying to run on HPC). As this process is lightweight in compute, storage and time, running on local machines with the following options might solve the issue: +If process `FUSIONREPORT_DOWNLOAD` times out, it could be due to network restriction (for example if trying to run on HPC). As this process is lightweight in cpu, memory and time, running on local machines with the following options might solve the issue: ```bash nextflow run nf-core/rnafusion \ @@ -85,7 +79,7 @@ nextflow run nf-core/rnafusion \ --outdir ``` -Adjustments for compute requirements can be done by feeding a custom configuration with `-c /PATH/TO/CUSTOM/CONFIG`. +Adjustments for cpu and memory requirements can be done by feeding a custom configuration with `-c /PATH/TO/CUSTOM/CONFIG`. Where the custom configuration could look like (adaptation to local machine necessary): ```text @@ -100,17 +94,36 @@ process { The four `fusion-report` files: `cosmic.db`, `fusiongdb.db`, `fusiongdb2.db`, `mitelman.db` should then be copied into the HPC `/references/fusion_report_db`. -#### Non-human references +## Running the pipeline -Non-human references, not supported by default, can be built manually and fed to rnafusion using the parameter `--_ref`. +### Samplesheet input -#### STAR-Fusion references downloaded vs built +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. The pipeline will detect whether a sample is single- or paired-end from the samplesheet - the `fastq_2` column is empty for single-end. The samplesheet has to be a comma-separated file (.csv) but can have as many columns as you desire. There is a strict requirement for the first 4 columns to match those defined in the table below with the header row included. +A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. -By default STAR-Fusion references are **built**. You can also download them from [CTAT](https://github.com/NCIP/Trinity_CTAT/wiki) by using the flag `--starfusion_build FALSE` for both reference building and fusion detection. This allows more flexibility for different organisms but **be aware that STAR-Fusion reference download is not recommended as not fully tested!** +```console +sample,fastq_1,fastq_2,strandedness +CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward +CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,forward +CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,forward +TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,forward +TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,forward +TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,forward +TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,forward +``` -### 2. Detecting fusions +As you can see above for multiple runs of the same sample, the `sample` name has to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. -This step can either be run using all fusion detection tools or specifying individual tools. Visualisation tools will be run on all fusions detected. To run all tools (`arriba`, `fusioncatcher`, `pizzly`, `squid`, `starfusion`, `stringtie`) use the `--all` parameter: +| Column | Description | +| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `strandedness` | Strandedness: forward or reverse. | + +### Starting commands + +The pipeline can either be run using all fusion detection tools or specifying individual tools. Visualisation tools will be run on all fusions detected. To run all tools (`arriba`, `fusioncatcher`, `pizzly`, `squid`, `starfusion`, `stringtie`) use the `--all` parameter: ```bash nextflow run nf-core/rnafusion \ @@ -120,11 +133,7 @@ nextflow run nf-core/rnafusion \ --outdir ``` -> **IMPORTANT: Either `--all` or `--`** is necessary to run detection tools - -`--genomes_base` should be the path to the directory containing the folder `references/` that was built in step 1 `build_references`. - -Alternatively, to run only a specific detection tool use: `--tool`: +To run only a specific detection tool use: `--tool`: ```bash nextflow run nf-core/rnafusion \ @@ -134,11 +143,48 @@ nextflow run nf-core/rnafusion \ --outdir ``` +> **IMPORTANT: Either `--all` or `--`** is necessary to run detection tools + +`--genomes_base` should be the path to the directory containing the folder `references/` that was built with `--build_references`. + +Note that the pipeline will create the following files in your working directory: + +```bash +work # Directory containing the nextflow working files + # Finished results in specified location (defined with --outdir) +.nextflow_log # Log file from Nextflow +# Other nextflow hidden files, eg. history of pipeline runs and old logs. +``` + +If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. + +Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. + +> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). + +The above pipeline run specified with a params file in yaml format: + +```bash +nextflow run nf-core/rnafusion -profile docker -params-file params.yaml +``` + +with `params.yaml` containing: + +```yaml +input: './samplesheet.csv' +outdir: './results/' +<...> +``` + +You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + +### Options + #### Trimming There are 2 options to trim -1. fastp +1. Fastp In this case all tools use the trimmed reads. Quality and adapter trimming by default. In addition, tail trimming and adapter_fastq specification are possible. Example usage: ```bash @@ -152,7 +198,7 @@ nextflow run nf-core/rnafusion \ --adapter_fastq (optional) ``` -2. hard trimming +2. Hard trimming In this case, only reads fed to fusioncatcher are trimmed. This is a harsh workaround in case of high read-through. The recommended trimming is thus the fastp_trim one. The trimming is done at 75 bp from the tails. Example usage: ```bash @@ -199,7 +245,7 @@ GENE3--GENE4 #### Running FusionInspector only -FusionInspector can be run standalone with: +FusionInspector can be run as a standalone with: ```bash nextflow run nf-core/rnafusion \ @@ -227,7 +273,7 @@ nextflow run nf-core/rnafusion \ --outdir ``` -This will skip all QC-related processes. +This will skip all QC-related processes (metrics collection, `Qualimap`) #### Skipping visualisation @@ -246,83 +292,6 @@ This will skip all visualisation processes, including `fusion-report`, `FusionIn It is possible to give the output of each tool manually using the argument: `--_fusions PATH/TO/FUSION/FILE`: this feature need more testing, don't hesitate to open an issue if you encounter problems. -## Samplesheet input - -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use the `--input` parameter to specify its location. The pipeline will detect whether a sample is single- or paired-end from the samplesheet - the `fastq_2` column is empty for single-end. The samplesheet has to be a comma-separated file (.csv) but can have as many columns as you desire. There is a strict requirement for the first 4 columns to match those defined in the table below with the header row included. -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. - -```console -sample,fastq_1,fastq_2,strandedness -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz,forward -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz,forward -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz,,forward -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz,,forward -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz,,forward -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,,forward -``` - -| Column | Description | -| -------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `strandedness` | Strandedness: forward or reverse. | - -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. - -As you can see above for multiple runs of the same sample, the `sample` name has to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: - -```bash -sample,fastq_1,fastq_2,strandedness -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,forward -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz,forward -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz,forward -``` - -## Running the pipeline - -The typical command for running the pipeline is as follows. - -```bash -nextflow run nf-core/rnafusion --input ./samplesheet.csv --outdir ./results -profile docker -``` - -This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. - -Note that the pipeline will create the following files in your working directory: - -```bash -work # Directory containing the nextflow working files - # Finished results in specified location (defined with --outdir) -.nextflow_log # Log file from Nextflow -# Other nextflow hidden files, eg. history of pipeline runs and old logs. -``` - -If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. - -Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. - -> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). - -The above pipeline run specified with a params file in yaml format: - -```bash -nextflow run nf-core/rnafusion -profile docker -params-file params.yaml -``` - -with `params.yaml` containing: - -```yaml -input: './samplesheet.csv' -outdir: './results/' -<...> -``` - -You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). - -### Options - #### Set different `--limitSjdbInsertNsj` parameter There are two parameters to increase the `--limitSjdbInsertNsj` parameter if necessary: @@ -330,6 +299,11 @@ There are two parameters to increase the `--limitSjdbInsertNsj` parameter if nec - `--fusioncatcher_limitSjdbInsertNsj`, default: 2000000 - `--fusioninspector_limitSjdbInsertNsj`, default: 1000000 +Use the parameter `--cram` to compress the BAM files to CRAM for specific tools. Options: arriba, squid, starfusion. Leave no space between options: + +- `--cram arriba,squid,starfusion`, default: [] +- `--cram arriba` + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -338,13 +312,6 @@ When you run the above command, Nextflow automatically pulls the pipeline code f nextflow pull nf-core/rnafusion ``` -#### Compress to CRAM file - -Use the parameter `--cram` to compress the BAM files to CRAM for specific tools. Options: arriba, squid, starfusion. Leave no space between options: - -- `--cram arriba,squid,starfusion`, default: [] -- `--cram arriba` - ### Reproducibility It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. From 23945d30b6908ef1620d058bf90bad2500cd3a94 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 11 Sep 2023 16:34:36 +0200 Subject: [PATCH 060/264] update citations --- CITATIONS.md | 37 +++++++++++++++++++++++++++++------- README.md | 24 +++++++++++------------ assets/samplesheet.csv | 2 -- assets/samplesheet_valid.csv | 2 -- 4 files changed, 42 insertions(+), 23 deletions(-) delete mode 100644 assets/samplesheet.csv delete mode 100644 assets/samplesheet_valid.csv diff --git a/CITATIONS.md b/CITATIONS.md index dca1640e..42e5e50c 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,34 +10,57 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [Arriba](https://github.com/suhrig/arriba) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B, Toprak UH, Neumann O, Stenzinger A, Scholl C, Fröhling S, Brors B. Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Research. 2021 Mar 31;448-460. doi: 10.1101/gr.257246.119. Epub 2021 Jan 13. PubMed PMID: 33441414. -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +- [BEDOPS](https://bedops.readthedocs.io/en/latest/index.html) - convert2bed - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Neph S, Scott Kuehn M, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012 May, 28 (14): 1919-1920. doi: 10.1093/bioinformatics/bts277, PubMed PMID: PMID: 22576172. -- [Arriba](https://github.com/suhrig/arriba) +- [FastP](https://academic.oup.com/bioinformatics/article/34/17/i884/5093234) - > Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B, Toprak UH, Neumann O, Stenzinger A, Scholl C, Fröhling S, Brors B. Accurate and efficient detection of gene fusions from RNA sequencing data. - > Genome Research. 2021 Mar 31;448-460. doi: 10.1101/gr.257246.119. Epub 2021 Jan 13. PubMed PMID: 33441414; PubMed Central PMCID: PMC7919457. + > Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sept 34:17 (i884–i890), doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086. PubMed Central PMCID: PMC6129281 + +- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) + + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) > Nicorici D, Satalan M, Edgren H, Kangaspeska S, Murumagi A, Kallioniemi O, Virtanen S, Kilkku O. FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data. BioRxiv, 2014 Nov. doi: 10.1101/011650. +- [FusionInspector](https://github.com/FusionInspector/FusionInspector) + + > Haas BJ, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson JT, Gillani R, Kasif S, Regev A. Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector. Cell Reports Methods. 2023 May 3:5, doi: 10.1016/j.crmeth.2023.100467, PMID: 37323575 + - [Fusion-report](https://github.com/matq007/fusion-report) > Proks M, Genomic Profiling of a Comprehensive Nation-wide Collection of Childhood Solid Tumors, Master Thesis, Supervisors: Grøntved L, Díaz de Ståhl T, Nistér M, Ewels P, Garcia MU, Juhos S, University of Southern Denmark, 2019, unpublished. +- [GATK4](https://gatk.broadinstitute.org/hc/en-us) + + > Van der Auwera GA. Somatic variation discovery with GATK4. Proceedings of the American Association for Cancer Research Annual Meeting 2017. 2017 Apr 1-5. Cancer Res 2017;77(13 Suppl) doi:10.1158/1538-7445.AM2017-3590 + - [Kallisto](https://pachterlab.github.io/kallisto/) > Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 2016 Apr. 34, 525–527. doi:10.1038/nbt.3519. PMID: 27043002. +- [MegaFusion](https://github.com/J35P312/MegaFusion) + +- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) + + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + +- [picard-tools](http://broadinstitute.github.io/picard) + - [Pizzly](https://github.com/pmelsted/pizzly) Melsted P, Hateley S, Joseph IC, Pimentel H, Bray N, Pachter L. Fusion detection and quantification by pseudoalignment. BioRxiv, 2017 Jul. doi: 10.1101/166322. +- [Qualimap 2](https://pubmed.ncbi.nlm.nih.gov/26428292/) + + > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1. PubMed PMID: 26428292; PubMed Central PMCID: PMC4708105. + - [SAMtools](https://pubmed.ncbi.nlm.nih.gov/19505943/) > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. diff --git a/README.md b/README.md index 17559918..30f6e82b 100644 --- a/README.md +++ b/README.md @@ -41,22 +41,22 @@ In rnafusion the full-sized test includes reference building and fusion detectio 3. Reads quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 4. Optional trimming with [fastp](https://github.com/OpenGene/fastp) 5. Arriba subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [Arriba](https://github.com/suhrig/arriba) fusion detection + - [STAR](https://github.com/alexdobin/STAR) alignment + - [Arriba](https://github.com/suhrig/arriba) fusion detection 6. Pizzly subworkflow - - [Kallisto](https://pachterlab.github.io/kallisto/) quantification - - [Pizzly](https://github.com/pmelsted/pizzly) fusion detection + - [Kallisto](https://pachterlab.github.io/kallisto/) quantification + - [Pizzly](https://github.com/pmelsted/pizzly) fusion detection 7. Squid subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [Samtools view](http://www.htslib.org/): convert sam output from STAR to bam - - [Samtools sort](http://www.htslib.org/): bam output from STAR - - [SQUID](https://github.com/Kingsford-Group/squid) fusion detection - - [SQUID](https://github.com/Kingsford-Group/squid) annotate + - [STAR](https://github.com/alexdobin/STAR) alignment + - [Samtools view](http://www.htslib.org/): convert sam output from STAR to bam + - [Samtools sort](http://www.htslib.org/): bam output from STAR + - [SQUID](https://github.com/Kingsford-Group/squid) fusion detection + - [SQUID](https://github.com/Kingsford-Group/squid) annotate 8. STAR-fusion subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection + - [STAR](https://github.com/alexdobin/STAR) alignment + - [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection 9. Fusioncatcher subworkflow - - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection + - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection 10. StringTie subworkflow - [StringTie](https://ccb.jhu.edu/software/stringtie/) 11. Fusion-report diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv deleted file mode 100644 index 4f9acc40..00000000 --- a/assets/samplesheet.csv +++ /dev/null @@ -1,2 +0,0 @@ -sample,fastq_1,fastq_2,strandedness -test_rnafusion,https://github.com/nf-core/test-datasets/raw/d6cd12c9a69c148ef986d156d110f741df482b04/testdata/human/reads_1.fq.gz,https://github.com/nf-core/test-datasets/raw/d6cd12c9a69c148ef986d156d110f741df482b04/testdata/human/reads_2.fq.gz,forward diff --git a/assets/samplesheet_valid.csv b/assets/samplesheet_valid.csv deleted file mode 100644 index 4ac8f7b1..00000000 --- a/assets/samplesheet_valid.csv +++ /dev/null @@ -1,2 +0,0 @@ -sample,fastq_1,fastq_2,strandedness -test,https://github.com/nf-core/test-datasets/raw/rnafusion/testdata/human/reads_1.fq.gz,https://github.com/nf-core/test-datasets/raw/rnafusion/testdata/human/reads_2.fq.gz,forward From 92a777cc9c943130d4a747f0841edaf00efd39b2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 11 Sep 2023 16:34:57 +0200 Subject: [PATCH 061/264] correct copy-paste error --- modules/local/convert2bed/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/convert2bed/meta.yml b/modules/local/convert2bed/meta.yml index e578330b..31ff3649 100644 --- a/modules/local/convert2bed/meta.yml +++ b/modules/local/convert2bed/meta.yml @@ -4,7 +4,7 @@ description: convert from GTF to BED format tools: - convert2bed: description: convert from GTF to BED format - homepage: https://pachterlab.github.io/kallisto/ + homepage: https://github.com/bedops/bedops documentation: https://bedops.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/bedops/bedops doi: "" From 5de8ee2dcc60b6ed4c23781a9b6ebbc0cc066d5c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 11 Sep 2023 16:35:52 +0200 Subject: [PATCH 062/264] first steps in output update --- docs/output.md | 258 ++++++++++++++++++++++++++++--------------------- 1 file changed, 150 insertions(+), 108 deletions(-) diff --git a/docs/output.md b/docs/output.md index b7afedf1..8b4ad44d 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,7 +12,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Download and build references](#references) - Build references needed to run the rest of the pipeline - [STAR](#star) - Alignment for arriba, squid and STAR-fusion -- [Cat](#cat) - Concatenated fastq files per sample ID +- [Cat](#cat) - Concatenate fastq files per sample ID - [Arriba](#arriba) - Arriba fusion detection - [Pizzly](#pizzly) - Pizzly fusion detection - [Squid](#squid) - Squid fusion detection @@ -20,21 +20,23 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [StringTie](#stringtie) - StringTie assembly - [FusionCatcher](#fusioncatcher) - Fusion catcher fusion detection - [Samtools](#samtools) - SAM/BAM file manipulation -- [Fusion-report](#fusion-report) - Summary of the findings of each tool and comparison to COSMIC, Mitelman and FusionGBD databases -- [FusionInspector](#fusionInspector) - IGV-based visualisation tool for fusions filtered by fusion-report +- [Fusion-report](#fusion-report) - Summary of the findings of each tool and comparison to COSMIC, Mitelman, FusionGBD and FusionGDB2 databases +- [FusionInspector](#fusionInspector) - Supervised analysis of fusion predictions from fusion-report, recover and re-score evidence for such predictions - [Arriba visualisation](#arriba-visualisation) - Arriba visualisation report for FusionInspector fusions -- [Qualimap](#qualimap) - Quality control of alignment -- [Picard](#picard) - Collect metrics +- [Qualimap](#qualimap) - Quality control of alignments +- [Picard](#picard) - Collect QC metrics - [FastQC](#fastqc) - Raw read quality control -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline +- [MultiQC](#multiqc) - Aggregate reports describing QC results from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution -### Download and build references +## Download and build references
    -Output files +Output reference files and folder structure + +### References directory structure -- `genomes_base/` +- `references/` - `arriba` - `blacklist_hg38_GRCh38_v2.1.0.tsv.gz` - `protein_domains_hg38_GRCh38_v2.1.0.gff3` @@ -64,13 +66,132 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
    +## Main pipeline workflow + +> If no argument is specified here, the tool was used with default parameters. + +### Directory structure + +```text +{outdir} +├── arriba +├── arriba_visualisation +├── cram_arriba +├── cram_starfusion +├── cram_squid +├── fastp +├── fastqc +├── fusioncatcher +├── fusioninspector +├── fusionreport +├── kallisto_quant +├── megafusion +├── multiqc +├── picard +├── pizzly +├── pipeline_info +├── pizzly +├── qualimap +├── samtools_sort_for_arriba +├── squid +├── star_for_arriba +├── star_for_starfusion +├── star_for_squid +├── starfusion +└── work +.nextflow.log +``` + +### Arriba + +[Arriba](https://arriba.readthedocs.io/en/latest/) is used for i) detect gene fusions and ii) create a PDF report for the fusions found (visualisation): + +#### Detection + +
    +Output files + +- `arriba/` + - `.arriba.fusions.tsv` - contains the identified fusions + - `.arriba.fusions.discarded.tsv` + +
    + +#### Visualisation + +
    +Output files + +- `arriba_visualisation/` + - `.pdf` + +
    + +### Cat + +
    +Output files + +- `cat/` + - `_1.merged.fastq.gz` + - `_2.merged.fastq.gz` + +
    + +If multiple libraries or runs have been provided for the same sample in the input samplesheet (e.g. to increase sequencing depth) then these will be merged at the very beginning of the pipeline in order to have consistent sample naming throughout the pipeline. Please refer to the [usage](https://nf-co.re/rnafusion/usage#samplesheet-input) documentation to see how to specify these samples in the input samplesheet. + +### FastP + +### Kallisto + +
    +Output files + +- `kallisto` + - `.kallisto_quant.fusions.txt` + +
    + +### Pizzly + +Pizzly uses the following arguments: + +```bash +-k 31 \ +--align-score 2 \ +--insert-size 400 \ +--cache index.cache.txt +``` + +
    +Output files + +- `pizzly` + - `.pizzly.txt` - contains the identified fusions + - `.pizzly.unfiltered.json` + +
    + +### Squid + +Squid is run in two steps: i) fusion detection and ii) fusion annotation but the output is in a common `squid` directory + +
    +Output files + +- `squid` + - `.squid.fusions_sv.txt` - contains the identified fusions + - `.squid.fusions.annotated.txt`- contains the identified fusions annotated + +
    + ### STAR STAR is used to align to genome reference -STAR is run 3 times: +STAR is run for 3 tools: -For arriba with the parameters: +For `arriba` with the parameters: ```bash --readFilesCommand zcat \ @@ -91,7 +212,7 @@ For arriba with the parameters: --chimMultimapNmax 50 ``` -For squid with the parameters: +For `squid` with the parameters: ```bash --twopassMode Basic \ @@ -105,7 +226,7 @@ For squid with the parameters: --readFilesCommand zcat ``` -For STAR-fusion with the parameters: +For `STAR-fusion` with the parameters: ```bash --twopassMode Basic \ @@ -132,112 +253,33 @@ For STAR-fusion with the parameters: --chimOutType Junctions ``` -> STAR_FOR_STARFUSION uses `${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.chr.gtf` whereas STAR_FOR_ARRIBA and STAR_FOR_SQUID use `${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.gtf` - -
    -Output files - -- `star_for_` -_ **Common** -_ `.Log.final.out` -_ `.Log.progress.out` -_ `.SJ.out.tab` -_ **For arriba:** -_ `.Aligned.out.bam` -_ **For squid:** -_ `.Aligned.sortedByCoord.out.bam` -_ `.Chimeric.out.sam` -_ `.unmapped_1.fastq.gz` -_ `.unmapped_2.fastq.gz` -_ **For starfusion:** -_ `.Aligned.sortedByCoord.out.bam` -_ `.Chimeric.out.junction` -
    - -### Cat - -Cat is used to concatenate fastq files belonging to the same sample. - -
    -Output files - -- `cat` - - `_1.merged.fastq.gz` - - `_2.merged.fastq.gz` - -
    - -### Arriba - -Arriba is used for i) detect fusion and ii) output a PDF report for the fusions found (visualisation): - -#### Detection - -
    -Output files - -- `arriba` - - `.arriba.fusions.tsv` - contains the identified fusions - - `.arriba.fusions.discarded.tsv` - -
    - -#### Visualisation - -
    -Output files - -- `arriba_visualisation` - - `.pdf` - -
    - -### Pizzly - -The first step of the pizzly workflow is to run `kallisto quant`: - -#### Kallisto +> STAR_FOR_STARFUSION uses `${params.ensembl}/Homo_sapiens.GRCh38.${params.ensembl_version}.chr.gtf` whereas STAR_FOR_ARRIBA and STAR_FOR_SQUID use `${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.gtf`
    Output files -- `kallisto` - - `.kallisto_quant.fusions.txt` - -
    - -Pizzly refines kallisto output. +**Common** -#### Pizzly - -Pizzly uses the following arguments: - -```bash --k 31 \ ---align-score 2 \ ---insert-size 400 \ ---cache index.cache.txt -``` - -
    -Output files +- `star_for_` +- `.Log.final.out` +- `.Log.progress.out` +- `.SJ.out.tab` -- `pizzly` - - `.pizzly.txt` - contains the identified fusions - - `.pizzly.unfiltered.json` +**For arriba:** -
    +- `.Aligned.out.bam` -### Squid +**For squid:** -Squid is run in two steps: i) fusion detection and ii) fusion annotation but the output is in a common `squid` directory. +- `.Aligned.sortedByCoord.out.bam` +- `.Chimeric.out.sam` +- `.unmapped_1.fastq.gz` +- `.unmapped_2.fastq.gz` -
    -Output files + **For starfusion:** -- `squid` - - `.squid.fusions_sv.txt` - contains the identified fusions - - `.squid.fusions.annotated.txt`- contains the identified fusions annotatedvi +- `.Aligned.sortedByCoord.out.bam` +- `.Chimeric.out.junction`
    From d7f36fe7f746140cba5aa2d2be193ed5f564d78f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 10:41:39 +0200 Subject: [PATCH 063/264] update meta descriptions --- modules/local/fusionreport/detect/meta.yml | 2 +- modules/local/megafusion/meta.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/fusionreport/detect/meta.yml b/modules/local/fusionreport/detect/meta.yml index f3d5cd88..7b9de84c 100644 --- a/modules/local/fusionreport/detect/meta.yml +++ b/modules/local/fusionreport/detect/meta.yml @@ -4,7 +4,7 @@ keywords: - sort tools: - fusionreport: - description: fusionreport + description: Tool for parsing outputs from fusion detection tools homepage: https://github.com/matq007/fusion-report documentation: https://matq007.github.io/fusion-report/#/ doi: "10.1101/011650" diff --git a/modules/local/megafusion/meta.yml b/modules/local/megafusion/meta.yml index a25cd74c..31343c7e 100644 --- a/modules/local/megafusion/meta.yml +++ b/modules/local/megafusion/meta.yml @@ -4,7 +4,7 @@ keywords: - sort tools: - fusionreport: - description: megafusion + description: Converts RNA fusion files to SV VCF and collects statistics and metrics in a VCF file. homepage: Adapted from https://github.com/J35P312/MegaFusion documentation: https://github.com/J35P312/MegaFusion doi: "" From b1ca2c450e407e1919455ff10281475263a7bb09 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 10:41:50 +0200 Subject: [PATCH 064/264] refine output --- docs/output.md | 369 ++++++++++++++++++++++++++++--------------------- 1 file changed, 208 insertions(+), 161 deletions(-) diff --git a/docs/output.md b/docs/output.md index 8b4ad44d..64b8923f 100644 --- a/docs/output.md +++ b/docs/output.md @@ -102,6 +102,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d .nextflow.log ``` +If no parameter are specified, the default is applied. + ### Arriba [Arriba](https://arriba.readthedocs.io/en/latest/) is used for i) detect gene fusions and ii) create a PDF report for the fusions found (visualisation): @@ -112,8 +114,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `arriba/` - - `.arriba.fusions.tsv` - contains the identified fusions - - `.arriba.fusions.discarded.tsv` + - `.arriba.fusions.tsv` - contains the identified fusions + - `.arriba.fusions.discarded.tsv` @@ -123,7 +125,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `arriba_visualisation/` - - `.pdf` + - `.pdf` @@ -133,14 +135,97 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d Output files - `cat/` - - `_1.merged.fastq.gz` - - `_2.merged.fastq.gz` + - `_1.merged.fastq.gz` + - `_2.merged.fastq.gz` If multiple libraries or runs have been provided for the same sample in the input samplesheet (e.g. to increase sequencing depth) then these will be merged at the very beginning of the pipeline in order to have consistent sample naming throughout the pipeline. Please refer to the [usage](https://nf-co.re/rnafusion/usage#samplesheet-input) documentation to see how to specify these samples in the input samplesheet. -### FastP +### Fastp + +If `--trim_fastp` is selected, [fastp](https://github.com/OpenGene/fastp) will filter low quality reads as well as bases at the 5' and 3' ends, trim adapters (automatically detected, but input with parameter `--adapter_fasta` is possible). 3' trimming is also possible via parameter `--trim_tail`. + +
    +Output files + +- `fastp` + - `_1.fastp.fastq.gz` + - `_2.fastp.fastq.gz` + - `.fastp.html` + - `.fastp.json` + - `.fastp.log` + +
    + +### FastQC + +
    +Output files + +- `fastqc/` + - `*_fastqc.html`: FastQC report containing quality metrics. + - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. + +
    + +[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). + +![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) + +![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) + +![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) + +> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. + +### FusionCatcher + +
    +Output files + +- `fusioncatcher` + - `.fusioncatcher.fusion-genes.txt` + - `.fusioncatcher.summary.txt` + - `.fusioncatcher.log` + +
    + +[FusionCatcher](https://github.com/ndaniel/fusioncatcher) searches for novel/known somatic fusion genes translocations, and chimeras in RNA-seq data. Possibility to use parameter `--fusioncatcher_limitSjdbInsertNsj` to modify limitSjdbInsertNsj. + +### FusionInspector + +
    +Output files + +- `fusioninspector` + - `.fusion_inspector_web.html` - visualisation report described in details [here](https://github.com/FusionInspector/FusionInspector/wiki/FusionInspector-Visualizations) + - `FusionInspector.log` + - `.FusionInspector.fusions.abridged.tsv` + +
    + +[FusionInspector](https://github.com/FusionInspector/FusionInspector/tree/master) performs a validation of fusion transcript predictions. Possibility to use `--fusioninspector_limitSjdbInsertNsj` to set limitSjdbInsertNsj to anything other than the default 1000000. + +### Fusion-report + +
    +Output files + +- `fusionreport` + - + - `.fusionreport.tsv` + - `.fusionreport_filtered.tsv` + - `_fusionreport_index.html` - general report for all filtered fusions + - `.fusions.csv` - index in csv format + - `_.html` - specific report for each filtered fusion + +
    + +[Fusion-report](https://github.com/matq007/fusion-report) is a tool for parsing outputs from fusion detection tools. +The score is explained [on the original fusion-report github page](https://matq007.github.io/fusion-report/#/score). + +`--fusionreport_filter` can be used to filter the output of fusion-report to fusions identified by at least 2 different tools. ### Kallisto @@ -148,11 +233,55 @@ If multiple libraries or runs have been provided for the same sample in the inpu Output files - `kallisto` - - `.kallisto_quant.fusions.txt` + - `.kallisto_quant.fusions.txt` -### Pizzly +Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. + +### Megafusion + +
    +Output files + +- `megafusion` + - `.vcf` - contains the fusions in vcf format with collected statistics. + +
    + +[Megafusion](https://github.com/J35P312/MegaFusion) converts RNA fusion files to SV VCF and collects statistics and metrics in a VCF file. + +### MultiQC + +
    +Output files + +- `multiqc/` + - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. + - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. + - `multiqc_plots/`: directory containing static images from the report in various formats. + +
    + +[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. + +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . + +### Picard + +
    +Output files + +Picard CollectRnaMetrics and picard MarkDuplicates share the same outpur directory. + +- `picard` + - `.MarkDuplicates.metrics.txt` - metrics from CollectRnaMetrics + - `_rna_metrics.txt` - metrics from MarkDuplicates + - `.bam` - BAM file with marked duplicates + +
    + +#### Pizzly Pizzly uses the following arguments: @@ -172,6 +301,58 @@ Pizzly uses the following arguments: +### Qualimap + +
    +Output files + +- `qualimap` + - `qualimapReport.html` - HTML report + - `rnaseq_qc_results.txt` - TXT results + - `css` - dir for html style + - `images_qualimapReport`- dir for html images + - `raw_data_qualimapReport` - dir for html raw data + +
    + +### Samtools + +#### Samtools view + +Samtools view is used to convert the chimeric SAM output from STAR_FOR_SQUID to BAM + +
    +Output files + +- `samtools_view_for_squid` + - `_chimeric.bam` - sorted BAM file + +
    + +#### Samtools sort + +Samtools sort is used to sort BAM files from STAR_FOR_STARFUSION (for arriba visualisation) and the chimeric BAM from STAR_FOR_SQUID + +
    +Output files + +- `samtools_sort_for_` + - `(_chimeric)_sorted.bam` - sorted BAM file + +
    + +#### Samtools index + +Samtools index is used to index BAM files from STAR_FOR_ARRIBA (for arriba visualisation) and STAR_FOR_STARFUSION (for QC) + +
    +Output files + +- `samtools_for_` + - `.(Aligned.sortedByCoord).out.bam.bai` - + +
    + ### Squid Squid is run in two steps: i) fusion detection and ii) fusion annotation but the output is in a common `squid` directory @@ -180,8 +361,8 @@ Squid is run in two steps: i) fusion detection and ii) fusion annotation but the Output files - `squid` - - `.squid.fusions_sv.txt` - contains the identified fusions - - `.squid.fusions.annotated.txt`- contains the identified fusions annotated + - `.squid.fusions_sv.txt` - contains the identified fusions + - `.squid.fusions.annotated.txt`- contains the identified fusions annotated @@ -250,7 +431,8 @@ For `STAR-fusion` with the parameters: --alignInsertionFlush Right \ --alignSplicedMateMapLminOverLmate 0 \ --alignSplicedMateMapLmin 30 \ ---chimOutType Junctions +--chimOutType Junctions \ +--quantMode GeneCounts ``` > STAR_FOR_STARFUSION uses `${params.ensembl}/Homo_sapiens.GRCh38.${params.ensembl_version}.chr.gtf` whereas STAR_FOR_ARRIBA and STAR_FOR_SQUID use `${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.gtf` @@ -261,36 +443,38 @@ For `STAR-fusion` with the parameters: **Common** - `star_for_` -- `.Log.final.out` -- `.Log.progress.out` -- `.SJ.out.tab` +- `.Log.final.out` +- `.Log.progress.out` +- `.SJ.out.tab` **For arriba:** -- `.Aligned.out.bam` +- `.Aligned.out.bam` **For squid:** -- `.Aligned.sortedByCoord.out.bam` -- `.Chimeric.out.sam` -- `.unmapped_1.fastq.gz` -- `.unmapped_2.fastq.gz` +- `.Aligned.sortedByCoord.out.bam` +- `.Chimeric.out.sam` +- `.unmapped_1.fastq.gz` +- `.unmapped_2.fastq.gz` **For starfusion:** -- `.Aligned.sortedByCoord.out.bam` -- `.Chimeric.out.junction` +- `.Aligned.sortedByCoord.out.bam` +- `.Chimeric.out.junction` +The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, params.read_length default is 100. + ### STAR-fusion
    Output files - `starfusion` - - `.starfusion.fusion_predictions.tsv` - contains the identified fusions - - `.starfusion.abridged.tsv` + - `.starfusion.fusion_predictions.tsv` - contains the identified fusions + - `.starfusion.abridged.tsv` - `- contains the identified fusions.starfusion.abridged.coding_effect.tsv`
    @@ -300,149 +484,12 @@ For `STAR-fusion` with the parameters:
    Output files -- `stringtie//stringtie.merged.gtf` - merged gtf from annotation and stringtie output gtfs -
    - -### FusionCatcher - -
    -Output files - -- `fusioncatcher` -_ `.fusioncatcher.fusion-genes.txt` -_ `.fusioncatcher.summary.txt` \* `.fusioncatcher.log` -
    - -### Samtools - -#### Samtools view - -Samtools view is used to convert the chimeric SAM output from STAR_FOR_SQUID to BAM - -
    -Output files - -- `samtools_view_for_squid` - - `_chimeric.bam` - sorted BAM file - -
    - -#### Samtools sort - -Samtools sort is used to sort BAM files from STAR_FOR_STARFUSION (for arriba visualisation) and the chimeric BAM from STAR_FOR_SQUID - -
    -Output files - -- `samtools_sort_for_` - - `(_chimeric)_sorted.bam` - sorted BAM file - -
    - -#### Samtools index - -Samtools index is used to index BAM files from STAR_FOR_ARRIBA (for arriba visualisation) and STAR_FOR_STARFUSION (for QC) - -
    -Output files - -- `samtools_for_` - - `.(Aligned.sortedByCoord).out.bam.bai` - - +- `stringtie//stringtie.merged.gtf` - merged gtf from annotation and stringtie output gtfs
    -### Fusion-report -
    -Output files -- `fusionreport` - - - - `.fusionreport.tsv` - - `.fusionreport_filtered.tsv` - - `index.html` - general report for all filtered fusions - - `.html` - specific report for each filtered fusion -
    - -The score is explained [on the original fusion-report github page](https://matq007.github.io/fusion-report/#/score). - -### FusionInspector - -
    -Output files - -- `fusioninspector` - - `.fusion_inspector_web.html` - visualisation report described in details [here](https://github.com/FusionInspector/FusionInspector/wiki/FusionInspector-Visualizations) - - `FusionInspector.log` - - `.FusionInspector.fusions.abridged.tsv` - -
    - -### Qualimap - -
    -Output files - -- `qualimap` - - `qualimapReport.html` - HTML report - - `rnaseq_qc_results.txt` - TXT results - - `css` - dir for html style - - `images_qualimapReport`- dir for html images - - `raw_data_qualimapReport` - dir for html raw data - -
    - -### Picard - -Picard CollectRnaMetrics and picard MarkDuplicates share the same outpur directory. - -
    -Output files - -- `picard` - - `.MarkDuplicates.metrics.txt` - metrics from CollectRnaMetrics - - `_rna_metrics.txt` - metrics from MarkDuplicates - - `.bam` - BAM file with marked duplicates - -
    - -### FastQC - -
    -Output files - -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. - -
    - -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). - -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) - -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) - -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) - -> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. - -### MultiQC - -
    -Output files - -- `multiqc/` - - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - - `multiqc_plots/`: directory containing static images from the report in various formats. - -
    - -[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. - -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . ### Pipeline information From 124c7f0b1e1031e6a1233cc74162b64eb7347546 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 11:02:31 +0200 Subject: [PATCH 065/264] prettify --- docs/output.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index 64b8923f..799e400b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -487,10 +487,6 @@ The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, par - `stringtie//stringtie.merged.gtf` - merged gtf from annotation and stringtie output gtfs - - - - ### Pipeline information
    From f76bd87c27dc31793e6bafbd41ef7f26db6d50de Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:22:35 +0200 Subject: [PATCH 066/264] Update docs/output.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 799e400b..4ab09184 100644 --- a/docs/output.md +++ b/docs/output.md @@ -272,7 +272,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
    Output files -Picard CollectRnaMetrics and picard MarkDuplicates share the same outpur directory. +Picard CollectRnaMetrics and picard MarkDuplicates share the same output directory. - `picard` - `.MarkDuplicates.metrics.txt` - metrics from CollectRnaMetrics From 02d1cf17975e6ac2019cefa2f1f28f99b50e0cd4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:22:47 +0200 Subject: [PATCH 067/264] Update docs/output.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 4ab09184..12a9eb44 100644 --- a/docs/output.md +++ b/docs/output.md @@ -102,7 +102,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d .nextflow.log ``` -If no parameter are specified, the default is applied. +If no parameters are specified, the default is applied. ### Arriba From 6f8ca3b0859744454e3ac8149f4200404a38bce3 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:23:07 +0200 Subject: [PATCH 068/264] Update docs/output.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- docs/output.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 12a9eb44..bd611b97 100644 --- a/docs/output.md +++ b/docs/output.md @@ -355,7 +355,7 @@ Samtools index is used to index BAM files from STAR_FOR_ARRIBA (for arriba visua ### Squid -Squid is run in two steps: i) fusion detection and ii) fusion annotation but the output is in a common `squid` directory +Squid is run in two steps: i) fusion detection and ii) fusion annotation, but the output is in a shared `squid` directory
    Output files From 9ef4faea86460b07d6f8e92dc4e9aa680fbe808f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:23:15 +0200 Subject: [PATCH 069/264] Update README.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 30f6e82b..f4ee6bee 100644 --- a/README.md +++ b/README.md @@ -102,7 +102,7 @@ nextflow run nf-core/rnafusion \ > **Notes:** > > - conda is not supported currently, run with singularity or docker -> - Paths need to be absolute +> - Paths need to be absolute. > - GRCh38 is the only supported reference > - Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. From 58302fdd7dd77a0daa11896e8f64e7a4ebbebdbc Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:23:23 +0200 Subject: [PATCH 070/264] Update README.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f4ee6bee..c0ed0b81 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,7 @@ In rnafusion the full-sized test includes reference building and fusion detectio As the reference building is computationally heavy (> 24h on HPC), it is recommended to test the pipeline with the `-stub` parameter (creation of empty files): -First build the references: +First, build the references: ```bash nextflow run nf-core/rnafusion \ From b9ffba9186829679b99a6348683f809c86defeba Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:23:30 +0200 Subject: [PATCH 071/264] Update README.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c0ed0b81..c2ce77ea 100644 --- a/README.md +++ b/README.md @@ -101,7 +101,7 @@ nextflow run nf-core/rnafusion \ > **Notes:** > -> - conda is not supported currently, run with singularity or docker +> - Conda is not currently supported; run with singularity or docker. > - Paths need to be absolute. > - GRCh38 is the only supported reference > - Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. From 2bee0ece1103efdd86aacef609562a14febcce0f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:23:37 +0200 Subject: [PATCH 072/264] Update README.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c2ce77ea..1954c52a 100644 --- a/README.md +++ b/README.md @@ -103,7 +103,7 @@ nextflow run nf-core/rnafusion \ > > - Conda is not currently supported; run with singularity or docker. > - Paths need to be absolute. -> - GRCh38 is the only supported reference +> - GRCh38 is the only supported reference. > - Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. > **Warning:** From 18b250a3d5cd0a68ac54641d8c708988bf34ca4e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:23:48 +0200 Subject: [PATCH 073/264] Update README.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1954c52a..cc9d97e3 100644 --- a/README.md +++ b/README.md @@ -104,7 +104,7 @@ nextflow run nf-core/rnafusion \ > - Conda is not currently supported; run with singularity or docker. > - Paths need to be absolute. > - GRCh38 is the only supported reference. -> - Single-end reads are to be use as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. +> - Single-end reads are to be used as last-resort. Paired-end reads are recommended. FusionCatcher cannot be used with single-end reads shorter than 130 bp. > **Warning:** > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those From e639142012ce4fda6f29c3107d84f1cbe78dc960 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:47:33 +0200 Subject: [PATCH 074/264] Update CHANGELOG.md Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b48c16e..21d68689 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,7 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `Arriba` visualisation now runs for FusionInspector (combined tools) results, not only `Arriba` results - Updated metro map with trimming options and placed `Arriba` visualisation after `FusionInspector` - Exit with error when using squid in combination with any ensembl version different from 102 -- Renaming [#395](https://github.com/nf-core/rnafusion/pull/395) +- Renamed output files [#395](https://github.com/nf-core/rnafusion/pull/395) - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out From e4a28baf27ed101eefee8fefa2b3c6a567535246 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:56:23 +0200 Subject: [PATCH 075/264] add output info in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 30f6e82b..961bd87d 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ ## Introduction -**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. +**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualiation document, a vcf data collection file and html and tsv reports. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results). From 3395388d96d13cac1fba84f7b36e137041f802bf Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 14:58:21 +0200 Subject: [PATCH 076/264] small typos --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1f8a9ee0..a6f3e750 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,9 @@ ## Introduction -**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualiation document, a vcf data collection file and html and tsv reports. +**nf-core/rnafusion** is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualiation document, a vcf data collection file, and html and tsv reports. -On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results). +On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/rnafusion/results). In rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from [here](https://github.com/nf-core/test-datasets/tree/rnafusion/testdata/human). From 061589ba23d622538dc2f7d2c82461982ee1168f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:12:22 +0200 Subject: [PATCH 077/264] add missing fusionreport stub and changelog update for previous PR --- CHANGELOG.md | 1 + modules/local/fusionreport/detect/main.nf | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 21d68689..fa68a69e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Use institutional configs by default [#381](https://github.com/nf-core/rnafusion/pull/381) - Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387) - Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387) +- Update and review documentation [#396](https://github.com/nf-core/rnafusion/pull/396) ### Fixed diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index e3ea5149..20db8c2f 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -53,7 +53,7 @@ process FUSIONREPORT { """ touch ${prefix}.fusionreport_filtered.tsv touch ${prefix}.fusionreport.tsv - touch index.html + touch ${prefix}_fusionreport_index.html touch AAA_BBB.html touch ${prefix}.fusions.csv touch ${prefix}.fusions.json From b4e2461f843674d15e696cea54d534aa5b5a5825 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:21:50 +0200 Subject: [PATCH 078/264] update megafusion output to _fusion_data.vcf --- CHANGELOG.md | 1 + conf/modules.config | 1 + 2 files changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fa68a69e..f26e61d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out - `fusion-report` index.html file to meta.id_fusionreport_index.html + - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf ### Fixed diff --git a/conf/modules.config b/conf/modules.config index 911fe292..b4dc96d6 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -143,6 +143,7 @@ process { } withName: MEGAFUSION { ext.when = {!params.fusioninspector_only} + ext.prefix = { "${meta.id}_fusion_data" } } From 91f65d0c8a5f8f3a068052ccf59a81c923f4d2e1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:25:16 +0200 Subject: [PATCH 079/264] prettify --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f26e61d6..f94b2031 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -47,7 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out - `fusion-report` index.html file to meta.id_fusionreport_index.html - - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf + - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf ### Fixed From c715953599fa43f4beaea3b7e5bc5518df44010f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:28:19 +0200 Subject: [PATCH 080/264] update modules from nf-core, update picard collectrnametrics container --- modules.json | 4 +-- .../local/picard/collectrnaseqmetrics/main.nf | 6 ++-- modules/nf-core/fastqc/tests/main.nf.test | 32 +++++++++++++++++++ modules/nf-core/picard/markduplicates/main.nf | 4 +++ 4 files changed, 41 insertions(+), 5 deletions(-) create mode 100644 modules/nf-core/fastqc/tests/main.nf.test diff --git a/modules.json b/modules.json index 38ba9c33..162a71b5 100644 --- a/modules.json +++ b/modules.json @@ -32,7 +32,7 @@ }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { @@ -62,7 +62,7 @@ }, "picard/markduplicates": { "branch": "master", - "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448", "installed_by": ["modules"] }, "qualimap/rnaseq": { diff --git a/modules/local/picard/collectrnaseqmetrics/main.nf b/modules/local/picard/collectrnaseqmetrics/main.nf index 5651c6c1..af0b8958 100644 --- a/modules/local/picard/collectrnaseqmetrics/main.nf +++ b/modules/local/picard/collectrnaseqmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTRNASEQMETRICS { tag "$meta.id" label 'process_medium' - conda "bioconda::picard=2.27.4" + conda "bioconda::picard=3.0.0 r::r-base" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:2.27.4--hdfd78af_0' : - 'quay.io/biocontainers/picard:2.27.4--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : + 'biocontainers/picard:3.0.0--hdfd78af_1' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test new file mode 100644 index 00000000..3961de60 --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -0,0 +1,32 @@ +nextflow_process { + + name "Test Process FASTQC" + script "modules/nf-core/fastqc/main.nf" + process "FASTQC" + tag "fastqc" + + test("Single-Read") { + + when { + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assert process.success + assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" + assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") + assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + } + + } + +} diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index facd7efb..ebfa0864 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -30,6 +30,9 @@ process PICARD_MARKDUPLICATES { } else { avail_mem = (task.memory.mega*0.8).intValue() } + + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ picard \\ -Xmx${avail_mem}M \\ @@ -48,6 +51,7 @@ process PICARD_MARKDUPLICATES { stub: def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ touch ${prefix}.bam touch ${prefix}.bam.bai From 5ee433c70a93ca98034ea5d72c118eabb65c7909 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:34:33 +0200 Subject: [PATCH 081/264] update changelog with picard update --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f94b2031..b61486da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Remove redundant indexing in starfusion and qc workflows [#387](https://github.com/nf-core/rnafusion/pull/387) - Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387) - Update and review documentation [#396](https://github.com/nf-core/rnafusion/pull/396) +- Update picard container for `PICARD_COLLECTRNASEQMETRICS` to 3.0.0 [#395](https://github.com/nf-core/rnafusion/pull/395) ### Fixed From fcde1cc563ff1780f2848bf24b611520610cfe35 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 13 Sep 2023 16:58:32 +0200 Subject: [PATCH 082/264] update version number and changelog release formatting --- CHANGELOG.md | 20 ++++++++++---------- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b61486da..0be1dba3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0dev +## v2.4.0 - [2023/09/18] ### Added @@ -28,7 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `samtools sort` and `samtools index` for `arriba` workflow were dispensable and were removed [#395](https://github.com/nf-core/rnafusion/pull/395) - Removed trimmed fastqc report from multiqc [#394](https://github.com/nf-core/rnafusion/pull/394) -## v2.3.0 = [2022/04/24] +## v2.3.0 - [2023/04/24] ### Added @@ -57,7 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed -## v2.2.0 - [2022/03/13] +## v2.2.0 - [2023/03/13] ### Added @@ -94,7 +94,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - FUSIONINSPECTOR_DEV process as the option fusioninspector_limitSjdbInsertNsj is part of the main starfusion release -## [2.1.0] nfcore/rnafusion - 2022/07/12 +## v2.1.0 - [2022/07/12] ### Added @@ -128,7 +128,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Removed -## [2.0.0] nfcore/rnafusion - 2022/05/19 +## v2.0.0 - [2022/05/19] Update to DSL2 and newer software/reference versions @@ -270,7 +270,7 @@ to - GRCh37 support. Subdirectory with params.genome are removed - Running with conda -## v1.3.0dev nfcore/rnafusion - 2020/07/15 +## v1.3.0 - [2020/07/15] - Using official STAR-Fusion container [#160](https://github.com/nf-core/rnafusion/issues/160) @@ -301,7 +301,7 @@ to --- -## [1.1.0] nfcore/rnafusion - 2020/02/10 +## v1.1.0 - [2020/02/10] - Fusion gene detection tools: - `Arriba v1.1.0` @@ -349,7 +349,7 @@ to --- -## [1.0.2] nfcore/rnafusion - 2019/05/13 +## v1.0.2 - [2019/05/13] ### Changed @@ -363,7 +363,7 @@ to --- -## [1.0.1] nfcore/rnafusion - 2019/04/06 +## v1.0.1 - [2019/04/06] ### Added @@ -391,7 +391,7 @@ to --- -## [1.0] nfcore/rnafusion - 2018/02/14 +## v1.0 - [2018/02/14] Version 1.0 marks the first production release of this pipeline under the nf-core flag. The pipeline includes additional help scripts to download references for fusion tools and Singularity images. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f02eb657..5e0f10e0 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnafusion-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 107eba8a..3a416e89 100644 --- a/nextflow.config +++ b/nextflow.config @@ -295,7 +295,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.4.0dev' + version = '2.4.0' doi = '' } From 16b702e04e73d690366a4543d72a1caac6bea416 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 15 Sep 2023 15:19:38 +0200 Subject: [PATCH 083/264] add descriptions of report files in tower.yml and correct output documentation --- docs/output.md | 14 +++++++------- tower.yml | 34 ++++++++++++++++++++++++++++++++-- 2 files changed, 39 insertions(+), 9 deletions(-) diff --git a/docs/output.md b/docs/output.md index bd611b97..fea293a2 100644 --- a/docs/output.md +++ b/docs/output.md @@ -125,7 +125,7 @@ If no parameters are specified, the default is applied. Output files - `arriba_visualisation/` - - `.pdf` + - `_combined_fusions_arriba_visualisation.pdf`
    @@ -149,7 +149,7 @@ If `--trim_fastp` is selected, [fastp](https://github.com/OpenGene/fastp) will f
    Output files -- `fastp` +- `fastp/` - `_1.fastp.fastq.gz` - `_2.fastp.fastq.gz` - `.fastp.html` @@ -245,7 +245,7 @@ Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or Output files - `megafusion` - - `.vcf` - contains the fusions in vcf format with collected statistics. + - `_fusion_data.vcf` - contains the fusions in vcf format with collected statistics.
    @@ -275,8 +275,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ Picard CollectRnaMetrics and picard MarkDuplicates share the same output directory. - `picard` - - `.MarkDuplicates.metrics.txt` - metrics from CollectRnaMetrics - - `_rna_metrics.txt` - metrics from MarkDuplicates + - `.MarkDuplicates.metrics.txt` - metrics from MarkDuplicates + - `_rna_metrics.txt` - metrics from CollectRnaMetrics - `.bam` - BAM file with marked duplicates
    @@ -462,6 +462,7 @@ For `STAR-fusion` with the parameters: - `.Aligned.sortedByCoord.out.bam` - `.Chimeric.out.junction` +- `.ReadsPerGene.out.tab`
    @@ -474,8 +475,7 @@ The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, par - `starfusion` - `.starfusion.fusion_predictions.tsv` - contains the identified fusions - - `.starfusion.abridged.tsv` - - `- contains the identified fusions.starfusion.abridged.coding_effect.tsv` + - `.starfusion.abridged.tsv`- contains the identified fusions.- `starfusion.abridged.coding_effect.tsv` diff --git a/tower.yml b/tower.yml index 787aedfe..5813f5d3 100644 --- a/tower.yml +++ b/tower.yml @@ -1,5 +1,35 @@ reports: multiqc_report.html: display: "MultiQC HTML report" - samplesheet.csv: - display: "Auto-created samplesheet with collated metadata and FASTQ paths" + "**/arriba/*.arriba.fusions.tsv": + display: "Arriba identified fusion TSV report" + "**/arriba_visualisation/*_combined_fusions_arriba_visualisation.pdf": + display: "PDF visualisation of the transcripts involved in predicted fusions" + "**/fastp/*fastp.html": + display: "Post fastp trimming HTML report" + "**/fusioncatcher/*.fusioncatcher.fusion-genes.txt": + display: "FusionCatcher identified fusion TXT report" + "**/fusioninspector/*.FusionInspector.fusions.abridged.tsv": + display: "FusionInspector TSV report" + "**/fusionreport/*/*_fusionreport_index.html": + display: "Fusion-report HTML report" + "**/megafusion/*_fusion_data.vcf": + display: "Collected statistics on each fusion fed to FusionInspector in VCF format" + "**/picard/*.MarkDuplicates.metrics.txt": + display: "Picard: Metrics from CollectRnaMetrics" + "**/picard/*_rna_metrics.txt": + display: "Picard: Metrics from MarkDuplicates" + "**/pizzly/*.pizzly.txt": + display: "Pizzly identified fusion TXT report" + "**/qualimap/qualimapReport.html": + display: "Qualimap HTML report from STAR_FOR_STARFUSION alignment" + "**/qualimap/rnaseq_qc_results.txt": + display: "Qualimap QC results from STAR_FOR_STARFUSION alignment in TXT format" + "**/squid/*.squid.fusions.annotated.txt": + display: "Squid identified fusion TXT report" + "**/star_for_starfusion/*ReadsPerGene.out.tab": + display: "Number of reads per gene" + "**/starfusion/*.starfusion.fusion_predictions.tsv": + display: "STAR-Fusion identified fusion TSV report" + "**/stringtie/*/*stringtie.merged.gtf": + display: "Merged GTFs from StringTie with annotations" From b6d7498707ae86ba1a02260b96e1ed3153959fad Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 15 Sep 2023 15:32:27 +0200 Subject: [PATCH 084/264] Update docs/output.md Co-authored-by: Vadym --- docs/output.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index fea293a2..be65328d 100644 --- a/docs/output.md +++ b/docs/output.md @@ -475,7 +475,8 @@ The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, par - `starfusion` - `.starfusion.fusion_predictions.tsv` - contains the identified fusions - - `.starfusion.abridged.tsv`- contains the identified fusions.- `starfusion.abridged.coding_effect.tsv` + - `.starfusion.abridged.tsv`- contains the identified fusions + - `starfusion.abridged.coding_effect.tsv` From 0b74b7fdd406a71c777cb7b5d2dee2cf681f44b1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 15 Sep 2023 15:34:16 +0200 Subject: [PATCH 085/264] fix formatting --- docs/output.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index fea293a2..4144891b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -475,7 +475,8 @@ The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, par - `starfusion` - `.starfusion.fusion_predictions.tsv` - contains the identified fusions - - `.starfusion.abridged.tsv`- contains the identified fusions.- `starfusion.abridged.coding_effect.tsv` + - `.starfusion.abridged.tsv` - contains the identified fusions abridged + - `starfusion.abridged.coding_effect.tsv` From f876680cd43623f2db9933f9819ca4380c34c0d0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 18 Sep 2023 10:56:44 +0200 Subject: [PATCH 086/264] Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases --- CHANGELOG.md | 1 + modules/local/fusionreport/detect/main.nf | 2 +- modules/local/fusionreport/download/main.nf | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0be1dba3..3d5b6e65 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385) - Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386) - The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388) +- Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases ### Removed diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 20db8c2f..38809803 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p2.1" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p4" input: diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index c54910a1..3ab1bc03 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p3" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p4" input: val(username) From 62f78bee79ef7eb80672314acad1fe6ab771daa4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 18 Sep 2023 11:35:58 +0200 Subject: [PATCH 087/264] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3d5b6e65..a07af52b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385) - Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386) - The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388) -- Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases +- Update fusionreport to 2.1.5p4 to fix 403 error in downloading databases [#403](https://github.com/nf-core/rnafusion/pull/403) ### Removed From f3a09cd2ddb67880b1b5a7439f318cc3c408b4da Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 20 Sep 2023 10:22:02 +0200 Subject: [PATCH 088/264] change release date, uncomment institutional config again (issue with merging) --- CHANGELOG.md | 2 +- conf/igenomes.config | 440 ------------------------------------------- nextflow.config | 10 +- 3 files changed, 6 insertions(+), 446 deletions(-) delete mode 100644 conf/igenomes.config diff --git a/CHANGELOG.md b/CHANGELOG.md index a07af52b..f216b4bc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0 - [2023/09/18] +## v2.4.0 - [2023/09/20] ### Added diff --git a/conf/igenomes.config b/conf/igenomes.config deleted file mode 100644 index 3f114377..00000000 --- a/conf/igenomes.config +++ /dev/null @@ -1,440 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines reference genomes using iGenome paths. - Can be used by any config that customises the base path using: - $params.igenomes_base / --igenomes_base ----------------------------------------------------------------------------------------- -*/ - -params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} diff --git a/nextflow.config b/nextflow.config index 3a416e89..994e96e3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -140,11 +140,11 @@ try { // Load nf-core/rnafusion custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! -// try { -// includeConfig "${params.custom_config_base}/pipeline/rnafusion.config" -// } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") -// } +try { + includeConfig "${params.custom_config_base}/pipeline/rnafusion.config" +} catch (Exception e) { + System.err.println("WARNING: Could not load nf-core/config/rnafusion profiles: ${params.custom_config_base}/pipeline/rnafusion.config") +} profiles { debug { dumpHashes = true From 3d24c125cdcb0a7b96a94bedb06b491626de894c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 22 Sep 2023 08:53:41 +0200 Subject: [PATCH 089/264] correct entry in changelog attributed to wrong release --- CHANGELOG.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f216b4bc..4c9ff036 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.4.0 - [2023/09/20] +## v2.4.0 - [2023/09/22] ### Added @@ -14,6 +14,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Output bai files in same directory as bam files [#387](https://github.com/nf-core/rnafusion/pull/387) - Update and review documentation [#396](https://github.com/nf-core/rnafusion/pull/396) - Update picard container for `PICARD_COLLECTRNASEQMETRICS` to 3.0.0 [#395](https://github.com/nf-core/rnafusion/pull/395) +- Renamed output files [#395](https://github.com/nf-core/rnafusion/pull/395) + - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation + - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba + - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out + - `fusion-report` index.html file to meta.id_fusionreport_index.html + - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf ### Fixed @@ -44,12 +50,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `Arriba` visualisation now runs for FusionInspector (combined tools) results, not only `Arriba` results - Updated metro map with trimming options and placed `Arriba` visualisation after `FusionInspector` - Exit with error when using squid in combination with any ensembl version different from 102 -- Renamed output files [#395](https://github.com/nf-core/rnafusion/pull/395) - - `Arriba` visualisation pdf from meta.id to meta.id_combined_fusions_arriba_visualisation - - cram file from output bam of `STAR_FOR_ARRIBA`: meta.id to meta.id_star_for_arriba - - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out - - `fusion-report` index.html file to meta.id_fusionreport_index.html - - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf ### Fixed From 7118fe979740fd1b96bde80aee2c9cc9e028665a Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 22 Sep 2023 11:51:28 +0200 Subject: [PATCH 090/264] replace picard/markduplicates module with gatk4/markduplicates --- conf/modules.config | 7 +- modules.json | 10 +-- modules/nf-core/gatk4/markduplicates/main.nf | 68 +++++++++++++++++ modules/nf-core/gatk4/markduplicates/meta.yml | 73 +++++++++++++++++++ modules/nf-core/picard/markduplicates/main.nf | 65 ----------------- .../nf-core/picard/markduplicates/meta.yml | 71 ------------------ subworkflows/local/qc_workflow.nf | 8 +- tower.yml | 2 +- 8 files changed, 157 insertions(+), 147 deletions(-) create mode 100644 modules/nf-core/gatk4/markduplicates/main.nf create mode 100644 modules/nf-core/gatk4/markduplicates/meta.yml delete mode 100644 modules/nf-core/picard/markduplicates/main.nf delete mode 100644 modules/nf-core/picard/markduplicates/meta.yml diff --git a/conf/modules.config b/conf/modules.config index b4dc96d6..f8ab151e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -157,8 +157,13 @@ process { } - withName: PICARD_MARKDUPLICATES { + withName: GATK4_MARKDUPLICATES { ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) } + publishDir = [ + path: { "${params.outdir}/picard" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] } withName: PIZZLY { diff --git a/modules.json b/modules.json index 162a71b5..c1686270 100644 --- a/modules.json +++ b/modules.json @@ -45,6 +45,11 @@ "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", "installed_by": ["modules"] }, + "gatk4/markduplicates": { + "branch": "master", + "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd", + "installed_by": ["modules"] + }, "kallisto/index": { "branch": "master", "git_sha": "699fa6f3002d922380615f3847198aeb57d8b6a9", @@ -60,11 +65,6 @@ "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", "installed_by": ["modules"] }, - "picard/markduplicates": { - "branch": "master", - "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448", - "installed_by": ["modules"] - }, "qualimap/rnaseq": { "branch": "master", "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f", diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf new file mode 100644 index 00000000..e4c01f9a --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -0,0 +1,68 @@ +process GATK4_MARKDUPLICATES { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::gatk4=4.4.0.0 bioconda::samtools=1.17" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0': + 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0' }" + + input: + tuple val(meta), path(bam) + path fasta + path fasta_fai + + output: + tuple val(meta), path("*cram"), emit: cram, optional: true + tuple val(meta), path("*bam"), emit: bam, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.bai"), emit: bai, optional: true + tuple val(meta), path("*.metrics"), emit: metrics + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}.bam" + + // If the extension is CRAM, then change it to BAM + prefix_bam = prefix.tokenize('.')[-1] == 'cram' ? "${prefix.substring(0, prefix.lastIndexOf('.'))}.bam" : prefix + + def input_list = bam.collect{"--INPUT $it"}.join(' ') + def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : "" + + def avail_mem = 3072 + if (!task.memory) { + log.info '[GATK MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + + // Using samtools and not Markduplicates to compress to CRAM speeds up computation: + // https://medium.com/@acarroll.dna/looking-at-trade-offs-in-compression-levels-for-genomics-tools-eec2834e8b94 + """ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + MarkDuplicates \\ + $input_list \\ + --OUTPUT ${prefix_bam} \\ + --METRICS_FILE ${prefix}.metrics \\ + --TMP_DIR . \\ + ${reference} \\ + $args + + # If cram files are wished as output, the run samtools for conversion + if [[ ${prefix} == *.cram ]]; then + samtools view -Ch -T ${fasta} -o ${prefix} ${prefix_bam} + rm ${prefix_bam} + samtools index ${prefix} + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml new file mode 100644 index 00000000..d3e75505 --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/meta.yml @@ -0,0 +1,73 @@ +name: gatk4_markduplicates +description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. +keywords: + - bam + - gatk4 + - markduplicates + - sort +tools: + - gatk4: + description: + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- + tool_dev_url: https://github.com/broadinstitute/gatk + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: Fasta file + pattern: "*.{fasta}" + - fasta_fai: + type: file + description: Fasta index file + pattern: "*.{fai}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + type: file + description: Marked duplicates BAM file + pattern: "*.{bam}" + - cram: + type: file + description: Marked duplicates CRAM file + pattern: "*.{cram}" + - bai: + type: file + description: BAM index file + pattern: "*.{bam.bai}" + - crai: + type: file + description: CRAM index file + pattern: "*.{cram.crai}" + - metrics: + type: file + description: Duplicate metrics file generated by GATK + pattern: "*.{metrics.txt}" + +authors: + - "@ajodeh-juma" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf deleted file mode 100644 index ebfa0864..00000000 --- a/modules/nf-core/picard/markduplicates/main.nf +++ /dev/null @@ -1,65 +0,0 @@ -process PICARD_MARKDUPLICATES { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::picard=3.0.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" - - input: - tuple val(meta), path(bam) - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - - output: - tuple val(meta), path("*.bam") , emit: bam - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.metrics.txt"), emit: metrics - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3072 - if (!task.memory) { - log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() - } - - if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - - """ - picard \\ - -Xmx${avail_mem}M \\ - MarkDuplicates \\ - $args \\ - --INPUT $bam \\ - --OUTPUT ${prefix}.bam \\ - --REFERENCE_SEQUENCE $fasta \\ - --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - """ - touch ${prefix}.bam - touch ${prefix}.bam.bai - touch ${prefix}.MarkDuplicates.metrics.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS - """ -} diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml deleted file mode 100644 index f7693d2f..00000000 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ /dev/null @@ -1,71 +0,0 @@ -name: picard_markduplicates -description: Locate and tag duplicate reads in a BAM file -keywords: - - markduplicates - - pcr - - duplicates - - bam - - sam - - cram -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ["MIT"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference genome fasta index - pattern: "*.{fai}" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" - - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" - - metrics: - type: file - description: Duplicate metrics file generated by picard - pattern: "*.{metrics.txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@projectoriented" - - "@ramprasadn" diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index bdf887d1..d9cd0a87 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -4,7 +4,7 @@ include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq/main' include { PICARD_COLLECTRNASEQMETRICS } from '../../modules/local/picard/collectrnaseqmetrics/main' -include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main' +include { GATK4_MARKDUPLICATES } from '../../modules/nf-core/gatk4/markduplicates/main' workflow QC_WORKFLOW { take: @@ -27,9 +27,9 @@ workflow QC_WORKFLOW { ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) ch_rnaseq_metrics = Channel.empty().mix(PICARD_COLLECTRNASEQMETRICS.out.metrics) - PICARD_MARKDUPLICATES(ch_bam_sorted, ch_fasta, ch_fai) - ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) - ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics) + GATK4_MARKDUPLICATES(ch_bam_sorted, ch_fasta, ch_fai) + ch_versions = ch_versions.mix(GATK4_MARKDUPLICATES.out.versions) + ch_duplicate_metrics = Channel.empty().mix(GATK4_MARKDUPLICATES.out.metrics) emit: diff --git a/tower.yml b/tower.yml index 5813f5d3..694a83ee 100644 --- a/tower.yml +++ b/tower.yml @@ -15,7 +15,7 @@ reports: display: "Fusion-report HTML report" "**/megafusion/*_fusion_data.vcf": display: "Collected statistics on each fusion fed to FusionInspector in VCF format" - "**/picard/*.MarkDuplicates.metrics.txt": + "**/gatk4/*.MarkDuplicates.metrics.txt": display: "Picard: Metrics from CollectRnaMetrics" "**/picard/*_rna_metrics.txt": display: "Picard: Metrics from MarkDuplicates" From 4c4f5002d7036df683c365906aa26616be70f801 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 22 Sep 2023 14:31:58 +0200 Subject: [PATCH 091/264] add insertsizemetrics to QC workflow --- modules.json | 5 ++ .../picard/collectinsertsizemetrics/main.nf | 61 +++++++++++++++++++ .../picard/collectinsertsizemetrics/meta.yml | 48 +++++++++++++++ subworkflows/local/qc_workflow.nf | 5 ++ tower.yml | 6 +- workflows/rnafusion.nf | 1 + 6 files changed, 125 insertions(+), 1 deletion(-) create mode 100644 modules/nf-core/picard/collectinsertsizemetrics/main.nf create mode 100644 modules/nf-core/picard/collectinsertsizemetrics/meta.yml diff --git a/modules.json b/modules.json index 162a71b5..a97f519a 100644 --- a/modules.json +++ b/modules.json @@ -55,6 +55,11 @@ "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", "installed_by": ["modules"] }, + "picard/collectinsertsizemetrics": { + "branch": "master", + "git_sha": "240937a2a9c30298110753292be041188891f2cb", + "installed_by": ["modules"] + }, "picard/collectwgsmetrics": { "branch": "master", "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf new file mode 100644 index 00000000..1d538fae --- /dev/null +++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf @@ -0,0 +1,61 @@ +process PICARD_COLLECTINSERTSIZEMETRICS { + tag "$meta.id" + label 'process_single' + + conda "bioconda::picard=3.0.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : + 'biocontainers/picard:3.0.0--hdfd78af_1' }" + + input: + tuple val(meta), path(bam) + + output: + tuple val(meta), path("*.txt"), emit: metrics + tuple val(meta), path("*.pdf"), emit: histogram + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def avail_mem = 3072 + if (!task.memory) { + log.info '[Picard CollectInsertSizeMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + """ + picard \\ + -Xmx${avail_mem}M \\ + CollectInsertSizeMetrics \\ + $args \\ + --INPUT $bam \\ + --OUTPUT ${prefix}.txt \\ + --Histogram_FILE ${prefix}.pdf \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(picard CollectInsertSizeMetrics --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ + + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.pdf + touch ${prefix}.txt + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(picard CollectInsertSizeMetrics --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ + + + +} diff --git a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml new file mode 100644 index 00000000..e611bdd4 --- /dev/null +++ b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml @@ -0,0 +1,48 @@ +name: "picard_collectinsertsizemetrics" +description: Collect metrics about the insert size distribution of a paired-end library. +keywords: + - metrics + - alignment + - insert + - statistics + - bam + +tools: + - "picard": + description: "Java tools for working with NGS data in the BAM format" + homepage: "https://broadinstitute.github.io/picard/" + documentation: "https://broadinstitute.github.io/picard/" + tool_dev_url: "https://github.com/broadinstitute/picard" + licence: "['MIT']" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - pdf: + type: file + description: Histogram plots of the insert size metrics computed by Picard + pattern: "*.pdf" + - metrics: + type: file + description: Values used by Picard to generate the insert size histograms + pattern: "*.txt" +authors: + - "@FerriolCalvet" diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index bdf887d1..b933a8be 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -31,12 +31,17 @@ workflow QC_WORKFLOW { ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) ch_duplicate_metrics = Channel.empty().mix(PICARD_MARKDUPLICATES.out.metrics) + PICARD_COLLECTINSERTSIZEMETRICS(ch_bam_sorted) + ch_versions = ch_versions.mix(PICARD_COLLECTINSERTSIZEMETRICS.out.versions) + ch_insertsize_metrics = Channel.empty().mix(PICARD_COLLECTINSERTSIZEMETRICS.out.metrics) + emit: versions = ch_versions.ifEmpty(null) qualimap_qc = ch_qualimap_qc rnaseq_metrics = ch_rnaseq_metrics duplicate_metrics = ch_duplicate_metrics + insertsize_metrics = ch_insertsize_metrics } diff --git a/tower.yml b/tower.yml index 5813f5d3..7160ccb7 100644 --- a/tower.yml +++ b/tower.yml @@ -18,7 +18,11 @@ reports: "**/picard/*.MarkDuplicates.metrics.txt": display: "Picard: Metrics from CollectRnaMetrics" "**/picard/*_rna_metrics.txt": - display: "Picard: Metrics from MarkDuplicates" + display: "GATK4: Metrics from MarkDuplicates" + "**/picard/*insert*size*metrics.txt": + display: "GATK4: Metrics from InsertSizeMetrics" + "**/picard/*pdf": + display: "GATK4: InsertSizeMetrics histogram" "**/pizzly/*.pizzly.txt": display: "Pizzly identified fusion TXT report" "**/qualimap/qualimapReport.html": diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 6f498e11..272e2f63 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -288,6 +288,7 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([])) From 035bcfbef5acca1fc2ba43bab742997b4b5e4d79 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 22 Sep 2023 15:55:47 +0200 Subject: [PATCH 092/264] replace qualimap/rnaseq with mosdepth --- modules.json | 10 +-- modules/nf-core/mosdepth/main.nf | 80 +++++++++++++++++ modules/nf-core/mosdepth/meta.yml | 109 +++++++++++++++++++++++ modules/nf-core/qualimap/rnaseq/main.nf | 63 ------------- modules/nf-core/qualimap/rnaseq/meta.yml | 52 ----------- subworkflows/local/qc_workflow.nf | 17 ++-- tower.yml | 2 + workflows/rnafusion.nf | 3 +- 8 files changed, 210 insertions(+), 126 deletions(-) create mode 100644 modules/nf-core/mosdepth/main.nf create mode 100644 modules/nf-core/mosdepth/meta.yml delete mode 100644 modules/nf-core/qualimap/rnaseq/main.nf delete mode 100644 modules/nf-core/qualimap/rnaseq/meta.yml diff --git a/modules.json b/modules.json index 162a71b5..fe82c5aa 100644 --- a/modules.json +++ b/modules.json @@ -50,6 +50,11 @@ "git_sha": "699fa6f3002d922380615f3847198aeb57d8b6a9", "installed_by": ["modules"] }, + "mosdepth": { + "branch": "master", + "git_sha": "ebb27711cd5f4de921244bfa81c676504072d31c", + "installed_by": ["modules"] + }, "multiqc": { "branch": "master", "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", @@ -65,11 +70,6 @@ "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448", "installed_by": ["modules"] }, - "qualimap/rnaseq": { - "branch": "master", - "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f", - "installed_by": ["modules"] - }, "samtools/faidx": { "branch": "master", "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", diff --git a/modules/nf-core/mosdepth/main.nf b/modules/nf-core/mosdepth/main.nf new file mode 100644 index 00000000..74db3a27 --- /dev/null +++ b/modules/nf-core/mosdepth/main.nf @@ -0,0 +1,80 @@ +process MOSDEPTH { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::mosdepth=0.3.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : + 'biocontainers/mosdepth:0.3.3--hdfd78af_1'}" + + input: + tuple val(meta), path(bam), path(bai), path(bed) + tuple val(meta2), path(fasta) + + output: + tuple val(meta), path('*.global.dist.txt') , emit: global_txt + tuple val(meta), path('*.summary.txt') , emit: summary_txt + tuple val(meta), path('*.region.dist.txt') , optional:true, emit: regions_txt + tuple val(meta), path('*.per-base.d4') , optional:true, emit: per_base_d4 + tuple val(meta), path('*.per-base.bed.gz') , optional:true, emit: per_base_bed + tuple val(meta), path('*.per-base.bed.gz.csi') , optional:true, emit: per_base_csi + tuple val(meta), path('*.regions.bed.gz') , optional:true, emit: regions_bed + tuple val(meta), path('*.regions.bed.gz.csi') , optional:true, emit: regions_csi + tuple val(meta), path('*.quantized.bed.gz') , optional:true, emit: quantized_bed + tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi + tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed + tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def reference = fasta ? "--fasta ${fasta}" : "" + def interval = bed ? "--by ${bed}" : "" + if (bed && args.contains("--by")) { + error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" + } + if (!bed && args.contains("--thresholds")) { + error "'--thresholds' can only be specified in conjunction with '--by'" + } + + """ + mosdepth \\ + --threads $task.cpus \\ + $interval \\ + $reference \\ + $args \\ + $prefix \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.global.dist.txt + touch ${prefix}.region.dist.txt + touch ${prefix}.summary.txt + touch ${prefix}.per-base.d4 + touch ${prefix}.per-base.bed.gz + touch ${prefix}.per-base.bed.gz.csi + touch ${prefix}.regions.bed.gz + touch ${prefix}.regions.bed.gz.csi + touch ${prefix}.quantized.bed.gz + touch ${prefix}.quantized.bed.gz.csi + touch ${prefix}.thresholds.bed.gz + touch ${prefix}.thresholds.bed.gz.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml new file mode 100644 index 00000000..adf3893f --- /dev/null +++ b/modules/nf-core/mosdepth/meta.yml @@ -0,0 +1,109 @@ +name: mosdepth +description: Calculates genome-wide sequencing coverage. +keywords: + - mosdepth + - bam + - cram + - coverage +tools: + - mosdepth: + description: | + Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. + documentation: https://github.com/brentp/mosdepth + doi: 10.1093/bioinformatics/btx699 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index for BAM/CRAM file + pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'test' ] + - bed: + type: file + description: BED file with intersected intervals + pattern: "*.{bed}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - global_txt: + type: file + description: Text file with global cumulative coverage distribution + pattern: "*.{global.dist.txt}" + - regions_txt: + type: file + description: Text file with region cumulative coverage distribution + pattern: "*.{region.dist.txt}" + - summary_txt: + type: file + description: Text file with summary mean depths per chromosome and regions + pattern: "*.{summary.txt}" + - per_base_bed: + type: file + description: BED file with per-base coverage + pattern: "*.{per-base.bed.gz}" + - per_base_csi: + type: file + description: Index file for BED file with per-base coverage + pattern: "*.{per-base.bed.gz.csi}" + - per_base_d4: + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" + - regions_bed: + type: file + description: BED file with per-region coverage + pattern: "*.{regions.bed.gz}" + - regions_csi: + type: file + description: Index file for BED file with per-region coverage + pattern: "*.{regions.bed.gz.csi}" + - quantized_bed: + type: file + description: BED file with binned coverage + pattern: "*.{quantized.bed.gz}" + - quantized_csi: + type: file + description: Index file for BED file with binned coverage + pattern: "*.{quantized.bed.gz.csi}" + - thresholds_bed: + type: file + description: BED file with the number of bases in each region that are covered at or above each threshold + pattern: "*.{thresholds.bed.gz}" + - thresholds_csi: + type: file + description: Index file for BED file with threshold coverage + pattern: "*.{thresholds.bed.gz.csi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" + - "@ramprasadn" + - "@matthdsm" diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf deleted file mode 100644 index 044c983f..00000000 --- a/modules/nf-core/qualimap/rnaseq/main.nf +++ /dev/null @@ -1,63 +0,0 @@ -process QUALIMAP_RNASEQ { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::qualimap=2.2.2d" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/qualimap:2.2.2d--1' : - 'biocontainers/qualimap:2.2.2d--1' }" - - input: - tuple val(meta), path(bam) - tuple val(meta2), path(gtf) - - output: - tuple val(meta), path("${prefix}"), emit: results - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def paired_end = meta.single_end ? '' : '-pe' - def memory = (task.memory.mega*0.8).intValue() + 'M' - - def strandedness = 'non-strand-specific' - if (meta.strandedness == 'forward') { - strandedness = 'strand-specific-forward' - } else if (meta.strandedness == 'reverse') { - strandedness = 'strand-specific-reverse' - } - """ - unset DISPLAY - mkdir -p tmp - export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp - qualimap \\ - --java-mem-size=$memory \\ - rnaseq \\ - $args \\ - -bam $bam \\ - -gtf $gtf \\ - -p $strandedness \\ - $paired_end \\ - -outdir $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') - END_VERSIONS - """ - - stub: - prefix = task.ext.prefix ?: "${meta.id}" - """ - mkdir ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml deleted file mode 100644 index 7738f08d..00000000 --- a/modules/nf-core/qualimap/rnaseq/meta.yml +++ /dev/null @@ -1,52 +0,0 @@ -name: qualimap_rnaseq -description: Evaluate alignment data -keywords: - - quality control - - qc - - rnaseq -tools: - - qualimap: - description: | - Qualimap 2 is a platform-independent application written in - Java and R that provides both a Graphical User Interface and - a command-line interface to facilitate the quality control of - alignment sequencing data and its derivatives like feature counts. - homepage: http://qualimap.bioinfo.cipf.es/ - documentation: http://qualimap.conesalab.org/doc_html/index.html - doi: 10.1093/bioinformatics/bts503 - licence: ["GPL-2.0-only"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome - pattern: "*.{gtf}" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - results: - type: directory - description: Qualimap results dir - pattern: "*/*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@FriederikeHanssen" diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index bdf887d1..204d78ca 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -2,7 +2,7 @@ // Check input samplesheet and get read channels // -include { QUALIMAP_RNASEQ } from '../../modules/nf-core/qualimap/rnaseq/main' +include { MOSDEPTH } from '../../modules/nf-core/mosdepth/main' include { PICARD_COLLECTRNASEQMETRICS } from '../../modules/local/picard/collectrnaseqmetrics/main' include { PICARD_MARKDUPLICATES } from '../../modules/nf-core/picard/markduplicates/main' @@ -19,9 +19,15 @@ workflow QC_WORKFLOW { main: ch_versions = Channel.empty() - QUALIMAP_RNASEQ(ch_bam_sorted, ch_chrgtf) - ch_versions = ch_versions.mix(QUALIMAP_RNASEQ.out.versions) - ch_qualimap_qc = Channel.empty().mix(QUALIMAP_RNASEQ.out.results) + ch_bam_sorted_indexed + .map { meta, bam, bai -> + return [meta, bam, bai, []] + }.set { ch_bam_sorted_indexed_bed } + + MOSDEPTH(ch_bam_sorted_indexed_bed, ch_fasta) + ch_versions = ch_versions.mix(MOSDEPTH.out.versions) + ch_mosdepth_summary = Channel.empty().mix(MOSDEPTH.out.summary_txt) + ch_mosdepth_global = Channel.empty().mix(MOSDEPTH.out.global_txt) PICARD_COLLECTRNASEQMETRICS(ch_bam_sorted_indexed, ch_refflat, ch_rrna_interval) ch_versions = ch_versions.mix(PICARD_COLLECTRNASEQMETRICS.out.versions) @@ -34,7 +40,8 @@ workflow QC_WORKFLOW { emit: versions = ch_versions.ifEmpty(null) - qualimap_qc = ch_qualimap_qc + mosdepth_summary = ch_mosdepth_summary + mosdepth_gobal = ch_mosdepth_global rnaseq_metrics = ch_rnaseq_metrics duplicate_metrics = ch_duplicate_metrics diff --git a/tower.yml b/tower.yml index 5813f5d3..b578f6c5 100644 --- a/tower.yml +++ b/tower.yml @@ -15,6 +15,8 @@ reports: display: "Fusion-report HTML report" "**/megafusion/*_fusion_data.vcf": display: "Collected statistics on each fusion fed to FusionInspector in VCF format" + "**/mosdepth/*.mosdepth.summary.txt": + display: "All samples summary of mean depths per chromosome and within specified regions per chromosome" "**/picard/*.MarkDuplicates.metrics.txt": display: "Picard: Metrics from CollectRnaMetrics" "**/picard/*_rna_metrics.txt": diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 6f498e11..266bc3cd 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -284,7 +284,8 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.qualimap_qc.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.mosdepth_summary.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.mosdepth_gobal.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([])) From 992636f642af8e6ee4b3cfac9fa15f4c4b5c4112 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 25 Sep 2023 10:37:48 +0200 Subject: [PATCH 093/264] remove squid/pizzly first steps --- .github/workflows/awsfulltest.yml | 94 -------------------- .github/workflows/awstest.yml | 98 --------------------- .github/workflows/ci.yml | 28 ------ CITATIONS.md | 11 --- README.md | 28 ++---- bin/megafusion.py | 10 +-- containers/arriba/Dockerfile | 14 --- containers/arriba/environment.yml | 14 --- containers/ericscript/Dockerfile | 17 ---- containers/ericscript/environment.yml | 8 -- containers/fusioncatcher/Dockerfile | 49 ----------- containers/pizzly/Dockerfile | 14 --- containers/pizzly/environment.yml | 9 -- containers/squid/Dockerfile | 19 ---- containers/squid/environment.yml | 11 --- docs/output.md | 83 +---------------- docs/usage.md | 8 +- modules.json | 5 -- modules/local/fusionreport/detect/main.nf | 4 +- modules/local/fusionreport/detect/meta.yml | 8 -- modules/local/kallisto/quant/main.nf | 47 ---------- modules/local/kallisto/quant/meta.yml | 44 --------- modules/local/pizzly/detect/main.nf | 49 ----------- modules/local/pizzly/detect/meta.yml | 44 --------- modules/local/pizzly/download/main.nf | 40 --------- modules/local/squid/annotate/main.nf | 41 --------- modules/local/squid/annotate/meta.yml | 36 -------- modules/local/squid/detect/main.nf | 40 --------- modules/local/squid/detect/meta.yml | 41 --------- modules/nf-core/kallisto/index/main.nf | 44 --------- modules/nf-core/kallisto/index/meta.yml | 43 --------- nextflow.config | 6 -- nextflow_schema.json | 32 +------ subworkflows/local/fusionreport_workflow.nf | 4 - subworkflows/local/pizzly_workflow.nf | 37 -------- subworkflows/local/squid_workflow.nf | 80 ----------------- tower.yml | 4 - workflows/build_references.nf | 7 +- workflows/rnafusion.nf | 25 ------ 39 files changed, 21 insertions(+), 1175 deletions(-) delete mode 100644 containers/arriba/Dockerfile delete mode 100644 containers/arriba/environment.yml delete mode 100644 containers/ericscript/Dockerfile delete mode 100644 containers/ericscript/environment.yml delete mode 100644 containers/fusioncatcher/Dockerfile delete mode 100644 containers/pizzly/Dockerfile delete mode 100644 containers/pizzly/environment.yml delete mode 100644 containers/squid/Dockerfile delete mode 100644 containers/squid/environment.yml delete mode 100644 modules/local/kallisto/quant/main.nf delete mode 100644 modules/local/kallisto/quant/meta.yml delete mode 100644 modules/local/pizzly/detect/main.nf delete mode 100644 modules/local/pizzly/detect/meta.yml delete mode 100644 modules/local/pizzly/download/main.nf delete mode 100644 modules/local/squid/annotate/main.nf delete mode 100644 modules/local/squid/annotate/meta.yml delete mode 100644 modules/local/squid/detect/main.nf delete mode 100644 modules/local/squid/detect/meta.yml delete mode 100644 modules/nf-core/kallisto/index/main.nf delete mode 100644 modules/nf-core/kallisto/index/meta.yml delete mode 100644 subworkflows/local/pizzly_workflow.nf delete mode 100644 subworkflows/local/squid_workflow.nf diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 31c6cd5f..f25848e7 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -62,53 +62,6 @@ jobs: tower_action_*.log tower_action_*.json - - name: Launch build squid workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "squid": true, - "build_references": true - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch squid workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "squid": true, - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - name: Launch build starfusion workflow via tower uses: seqeralabs/action-tower-launch@v2 with: @@ -203,53 +156,6 @@ jobs: tower_action_*.log tower_action_*.json - - name: Launch build pizzly workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "pizzly": true, - "build_references": true - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch pizzly workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "pizzly": true, - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - name: Launch stringtie workflow via tower uses: seqeralabs/action-tower-launch@v2 with: diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 003f6786..d43fe90b 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -61,55 +61,6 @@ jobs: tower_action_*.log tower_action_*.json - - name: Launch build squid workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "squid": true, - "stub": true, - "build_references": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch squid workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "squid": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - name: Launch build starfusion workflow via tower uses: seqeralabs/action-tower-launch@v2 with: @@ -208,55 +159,6 @@ jobs: tower_action_*.log tower_action_*.json - - name: Launch build pizzly workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "pizzly": true, - "build_references": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch pizzly workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "pizzly": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - name: Launch stringtie workflow via tower uses: seqeralabs/action-tower-launch@v2 with: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e62dcf41..d31089a7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,34 +49,6 @@ jobs: --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - name: Dry test squid build - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ - --outdir /home/runner/work/rnafusion/rnafusion/results --squid \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test squid - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --squid \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test pizzly build - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ - --outdir /home/runner/work/rnafusion/rnafusion/results --pizzly \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test pizzly - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --pizzly \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - name: Dry test fusioncatcher build run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ diff --git a/CITATIONS.md b/CITATIONS.md index 42e5e50c..2b666093 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -42,10 +42,6 @@ > Van der Auwera GA. Somatic variation discovery with GATK4. Proceedings of the American Association for Cancer Research Annual Meeting 2017. 2017 Apr 1-5. Cancer Res 2017;77(13 Suppl) doi:10.1158/1538-7445.AM2017-3590 -- [Kallisto](https://pachterlab.github.io/kallisto/) - - > Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology 2016 Apr. 34, 525–527. doi:10.1038/nbt.3519. PMID: 27043002. - - [MegaFusion](https://github.com/J35P312/MegaFusion) - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) @@ -54,9 +50,6 @@ - [picard-tools](http://broadinstitute.github.io/picard) -- [Pizzly](https://github.com/pmelsted/pizzly) - Melsted P, Hateley S, Joseph IC, Pimentel H, Bray N, Pachter L. Fusion detection and quantification by pseudoalignment. BioRxiv, 2017 Jul. doi: 10.1101/166322. - - [Qualimap 2](https://pubmed.ncbi.nlm.nih.gov/26428292/) > Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1. PubMed PMID: 26428292; PubMed Central PMCID: PMC4708105. @@ -65,10 +58,6 @@ > Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PubMed PMID: 19505943; PubMed Central PMCID: PMC2723002. -- [Squid](https://github.com/Kingsford-Group/squid) - - > Ma C, Shao M, Kingsford C. SQUID: transcriptomic structural variation detection from RNA-seq. Genome Biol 2028 Apr. 19, 52. doi: 10.1186/s13059-018-1421-5. PubMed PMID: 29650026. PubMed Central PMCID: PMC5896115. - - [STAR](https://pubmed.ncbi.nlm.nih.gov/23104886/) > Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905. diff --git a/README.md b/README.md index a6f3e750..b54f6e2c 100644 --- a/README.md +++ b/README.md @@ -30,9 +30,8 @@ In rnafusion the full-sized test includes reference building and fusion detectio 2. Create [STAR](https://github.com/alexdobin/STAR) index 3. Download [Arriba](https://github.com/suhrig/arriba) references 4. Download [FusionCatcher](https://github.com/ndaniel/fusioncatcher) references -5. Download [Pizzly](https://github.com/pmelsted/pizzly) references ([kallisto](https://pachterlab.github.io/kallisto/manual) index) -6. Download and build [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) references -7. Download [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) DBs +5. Download and build [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) references +6. Download [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) DBs #### Main workflow @@ -43,31 +42,22 @@ In rnafusion the full-sized test includes reference building and fusion detectio 5. Arriba subworkflow - [STAR](https://github.com/alexdobin/STAR) alignment - [Arriba](https://github.com/suhrig/arriba) fusion detection -6. Pizzly subworkflow - - [Kallisto](https://pachterlab.github.io/kallisto/) quantification - - [Pizzly](https://github.com/pmelsted/pizzly) fusion detection -7. Squid subworkflow - - [STAR](https://github.com/alexdobin/STAR) alignment - - [Samtools view](http://www.htslib.org/): convert sam output from STAR to bam - - [Samtools sort](http://www.htslib.org/): bam output from STAR - - [SQUID](https://github.com/Kingsford-Group/squid) fusion detection - - [SQUID](https://github.com/Kingsford-Group/squid) annotate -8. STAR-fusion subworkflow +6. STAR-fusion subworkflow - [STAR](https://github.com/alexdobin/STAR) alignment - [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) fusion detection -9. Fusioncatcher subworkflow +7. Fusioncatcher subworkflow - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection -10. StringTie subworkflow +8. StringTie subworkflow - [StringTie](https://ccb.jhu.edu/software/stringtie/) -11. Fusion-report +9. Fusion-report - Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) -12. Post-processing and analysis of data +10. Post-processing and analysis of data - [FusionInspector](https://github.com/FusionInspector/FusionInspector) - [Arriba](https://github.com/suhrig/arriba) visualisation - QC for mapped reads ([`QualiMap: BAM QC`](https://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html)) - Collect metrics ([`picard CollectRnaSeqMetrics`](https://gatk.broadinstitute.org/hc/en-us/articles/360037057492-CollectRnaSeqMetrics-Picard-) and ([`picard MarkDuplicates`](https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-)) -13. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) -14. Compress bam files to cram with [samtools view](http://www.htslib.org/) +11. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +12. Compress bam files to cram with [samtools view](http://www.htslib.org/) ## Usage diff --git a/bin/megafusion.py b/bin/megafusion.py index 76872b57..76a6a180 100755 --- a/bin/megafusion.py +++ b/bin/megafusion.py @@ -65,8 +65,6 @@ def header_def(sample): ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ -##INFO=\n\ -##INFO=\n\ ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ @@ -105,10 +103,6 @@ def read_build_fusionreport(fusionreport_file): fusion_report["arriba"] = "" if not "fusioncatcher" in fusion_report.columns: fusion_report["fusioncatcher"] = "" - if not "pizzly" in fusion_report.columns: - fusion_report["pizzly"] = "" - if not "squid" in fusion_report.columns: - fusion_report["squid"] = "" if not "starfusion" in fusion_report.columns: fusion_report["starfusion"] = "" return fusion_report @@ -140,7 +134,7 @@ def column_manipulation(df): # INFO df.loc[index, "INFO"] = ( "SVTYPE=BND;CHRA={};CHRB={};GENEA={};GENEB={};ORIENTATION={},{};FOUND_DB={};" - "ARRIBA={};FUSIONCATCHER={};PIZZLY={};SQUID={};STARFUSION={};TOOL_HITS={};SCORE={}".format( + "ARRIBA={};FUSIONCATCHER={};STARFUSION={};TOOL_HITS={};SCORE={}".format( row["chromosomeA"], row["chromosomeB"], row["geneA"], @@ -150,8 +144,6 @@ def column_manipulation(df): row["found_db"], row["arriba"], row["fusioncatcher"], - row["pizzly"], - row["squid"], row["starfusion"], row["tools_hits"], row["score"], diff --git a/containers/arriba/Dockerfile b/containers/arriba/Dockerfile deleted file mode 100644 index ea36d90f..00000000 --- a/containers/arriba/Dockerfile +++ /dev/null @@ -1,14 +0,0 @@ -FROM nfcore/base:1.9 - -LABEL authors="Martin Proks" \ - description="Docker image containing all requirements for nfcore/rnafusion pipeline" - -# Install the conda environment -COPY environment.yml / -RUN conda env create -f /environment.yml && conda clean -a - -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-rnafusion-arriba_1.2.0/bin:$PATH - -# Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-rnafusion-arriba_1.2.0 > nf-core-rnafusion-arriba_1.2.0.yml diff --git a/containers/arriba/environment.yml b/containers/arriba/environment.yml deleted file mode 100644 index 20a1024e..00000000 --- a/containers/arriba/environment.yml +++ /dev/null @@ -1,14 +0,0 @@ -name: nf-core-rnafusion-arriba_1.2.0 -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::arriba=1.2.0 - - bioconda::bioconductor-genomicalignments - - bioconda::bioconductor-genomicranges - - bioconda::samtools=1.9 - - bioconda::star=2.7.1a - - conda-forge::openssl=1.0 - - conda-forge::r-circlize - - conda-forge::readline=6.2 diff --git a/containers/ericscript/Dockerfile b/containers/ericscript/Dockerfile deleted file mode 100644 index 70b87c48..00000000 --- a/containers/ericscript/Dockerfile +++ /dev/null @@ -1,17 +0,0 @@ -FROM nfcore/base:1.9 - -LABEL authors="Martin Proks" \ - description="Docker image containing all requirements for nfcore/rnafusion pipeline" - -# Install the conda environment -COPY environment.yml / -RUN conda env create -f /environment.yml && conda clean -a - -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-rnafusion-ericscript_0.5.5/bin:$PATH - -# Ignore database check (https://github.com/nf-core/rnafusion/issues/119) -RUN echo 1 > /opt/conda/envs/nf-core-rnafusion-ericscript_0.5.5/share/ericscript-0.5.5-4/lib/data/_resources/.flag.dbexists - -# Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-rnafusion-ericscript_0.5.5 > nf-core-rnafusion-ericscript_0.5.5.yml diff --git a/containers/ericscript/environment.yml b/containers/ericscript/environment.yml deleted file mode 100644 index 1e76273c..00000000 --- a/containers/ericscript/environment.yml +++ /dev/null @@ -1,8 +0,0 @@ -name: nf-core-rnafusion-ericscript_0.5.5 -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::ericscript=0.5.5 - - conda-forge::ncurses=6.1 diff --git a/containers/fusioncatcher/Dockerfile b/containers/fusioncatcher/Dockerfile deleted file mode 100644 index 77efaf57..00000000 --- a/containers/fusioncatcher/Dockerfile +++ /dev/null @@ -1,49 +0,0 @@ -FROM ubuntu:18.04 - -LABEL Description="This image is used to run FusionCatcher" Version="1.33" - -RUN apt-get -y clean \ - && apt-get -y update \ - && apt-get -y install \ - automake \ - build-essential \ - bzip2 \ - cmake \ - curl \ - g++ \ - gawk \ - gcc \ - gzip \ - libc6-dev \ - libncurses5-dev \ - libtbb2 \ - libtbb-dev \ - make \ - parallel \ - pigz \ - python \ - python-dev \ - python-biopython \ - python-numpy \ - python-openpyxl \ - python-xlrd \ - tar \ - unzip \ - wget \ - zip \ - zlib1g \ - zlib1g-dev \ - zlibc \ - default-jdk \ - && apt-get -y clean - -WORKDIR /opt - -###################### -## INSTALLATION -###################### - -RUN wget --no-check-certificate http://sf.net/projects/fusioncatcher/files/bootstrap.py -O bootstrap.py \ - && python bootstrap.py -t -y -i /opt/fusioncatcher/v1.33/ - -ENV PATH /opt/fusioncatcher/v1.33/bin:$PATH diff --git a/containers/pizzly/Dockerfile b/containers/pizzly/Dockerfile deleted file mode 100644 index 0056bf9b..00000000 --- a/containers/pizzly/Dockerfile +++ /dev/null @@ -1,14 +0,0 @@ -FROM nfcore/base:1.9 - -LABEL authors="Martin Proks" \ - description="Docker image containing all requirements for nfcore/rnafusion pipeline" - -# Install the conda environment -COPY environment.yml / -RUN conda env create -f /environment.yml && conda clean -a - -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-rnafusion-pizzly_0.37.3/bin:$PATH - -# Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-rnafusion-pizzly_0.37.3 > nf-core-rnafusion-pizzly_0.37.3.yml diff --git a/containers/pizzly/environment.yml b/containers/pizzly/environment.yml deleted file mode 100644 index 79974871..00000000 --- a/containers/pizzly/environment.yml +++ /dev/null @@ -1,9 +0,0 @@ -name: nf-core-rnafusion-pizzly_0.37.3 -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::kallisto=0.44.0 - - bioconda::pizzly=0.37.3 - - conda-forge::pigz=2.3.4 diff --git a/containers/squid/Dockerfile b/containers/squid/Dockerfile deleted file mode 100644 index 20d390ee..00000000 --- a/containers/squid/Dockerfile +++ /dev/null @@ -1,19 +0,0 @@ -FROM nfcore/base:1.9 - -LABEL authors="Martin Proks" \ - description="Docker image containing all requirements for nfcore/rnafusion pipeline" - -# Install the conda environment -COPY environment.yml / -RUN conda env create -f /environment.yml && conda clean -a - -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-rnafusion-squid_1.5-star2.7.1a/bin:$PATH - -RUN cd /opt/conda/envs/nf-core-rnafusion-squid_1.5-star2.7.1a/bin \ - && wget https://raw.githubusercontent.com/Kingsford-Group/squid/f45c9025d41cffd982ecbbdd52844e5a4f074de9/utils/AnnotateSQUIDOutput.py \ - && chmod +x /opt/conda/envs/nf-core-rnafusion-squid_1.5-star2.7.1a/bin/AnnotateSQUIDOutput.py \ - && ln -s /opt/conda/envs/nf-core-rnafusion-squid_1.5-star2.7.1a/bin/python3 /bin/python - -# Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-rnafusion-squid_1.5-star2.7.1a > nf-core-rnafusion-squid_1.5-star2.7.1a.yml diff --git a/containers/squid/environment.yml b/containers/squid/environment.yml deleted file mode 100644 index 7385b163..00000000 --- a/containers/squid/environment.yml +++ /dev/null @@ -1,11 +0,0 @@ -name: nf-core-rnafusion-squid_1.5-star2.7.1a -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::samtools=1.9 - - bioconda::squid=1.5 - - bioconda::star=2.7.1a - - conda-forge::numpy=1.18.1 - - conda-forge::python=3.7.6 diff --git a/docs/output.md b/docs/output.md index 4144891b..f24d0db7 100644 --- a/docs/output.md +++ b/docs/output.md @@ -11,11 +11,9 @@ The directories listed below will be created in the results directory after the The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: - [Download and build references](#references) - Build references needed to run the rest of the pipeline -- [STAR](#star) - Alignment for arriba, squid and STAR-fusion +- [STAR](#star) - Alignment for arriba, and STAR-fusion - [Cat](#cat) - Concatenate fastq files per sample ID - [Arriba](#arriba) - Arriba fusion detection -- [Pizzly](#pizzly) - Pizzly fusion detection -- [Squid](#squid) - Squid fusion detection - [STAR-fusion](#starfusion) - STAR-fusion fusion detection - [StringTie](#stringtie) - StringTie assembly - [FusionCatcher](#fusioncatcher) - Fusion catcher fusion detection @@ -55,8 +53,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - `fusiongdb.db` - `fusiongdb2.db` - `mitelman.db` - - `pizzly` - - `kallisto` - file containing the kallisto index - `star` - dir with STAR index - `starfusion` - files and dirs used to build the index @@ -78,7 +74,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ├── arriba_visualisation ├── cram_arriba ├── cram_starfusion -├── cram_squid ├── fastp ├── fastqc ├── fusioncatcher @@ -88,15 +83,11 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ├── megafusion ├── multiqc ├── picard -├── pizzly ├── pipeline_info -├── pizzly ├── qualimap ├── samtools_sort_for_arriba -├── squid ├── star_for_arriba ├── star_for_starfusion -├── star_for_squid ├── starfusion └── work .nextflow.log @@ -281,26 +272,6 @@ Picard CollectRnaMetrics and picard MarkDuplicates share the same output directo -#### Pizzly - -Pizzly uses the following arguments: - -```bash --k 31 \ ---align-score 2 \ ---insert-size 400 \ ---cache index.cache.txt -``` - -
    -Output files - -- `pizzly` - - `.pizzly.txt` - contains the identified fusions - - `.pizzly.unfiltered.json` - -
    - ### Qualimap
    @@ -317,26 +288,14 @@ Pizzly uses the following arguments: ### Samtools -#### Samtools view - -Samtools view is used to convert the chimeric SAM output from STAR_FOR_SQUID to BAM - -
    -Output files - -- `samtools_view_for_squid` - - `_chimeric.bam` - sorted BAM file - -
    - #### Samtools sort -Samtools sort is used to sort BAM files from STAR_FOR_STARFUSION (for arriba visualisation) and the chimeric BAM from STAR_FOR_SQUID +Samtools sort is used to sort BAM files from STAR_FOR_STARFUSION (for arriba visualisation)
    Output files -- `samtools_sort_for_` +- `samtools_sort_for_` - `(_chimeric)_sorted.bam` - sorted BAM file
    @@ -353,19 +312,6 @@ Samtools index is used to index BAM files from STAR_FOR_ARRIBA (for arriba visua
    -### Squid - -Squid is run in two steps: i) fusion detection and ii) fusion annotation, but the output is in a shared `squid` directory - -
    -Output files - -- `squid` - - `.squid.fusions_sv.txt` - contains the identified fusions - - `.squid.fusions.annotated.txt`- contains the identified fusions annotated - -
    - ### STAR STAR is used to align to genome reference @@ -393,20 +339,6 @@ For `arriba` with the parameters: --chimMultimapNmax 50 ``` -For `squid` with the parameters: - -```bash ---twopassMode Basic \ ---chimOutType SeparateSAMold \ ---chimSegmentMin 20 \ ---chimJunctionOverhangMin 12 \ ---alignSJDBoverhangMin 10 \ ---outReadsUnmapped Fastx \ ---outSAMstrandField intronMotif \ ---outSAMtype BAM SortedByCoordinate \ ---readFilesCommand zcat -``` - For `STAR-fusion` with the parameters: ```bash @@ -435,7 +367,7 @@ For `STAR-fusion` with the parameters: --quantMode GeneCounts ``` -> STAR_FOR_STARFUSION uses `${params.ensembl}/Homo_sapiens.GRCh38.${params.ensembl_version}.chr.gtf` whereas STAR_FOR_ARRIBA and STAR_FOR_SQUID use `${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.gtf` +> STAR_FOR_STARFUSION uses `${params.ensembl}/Homo_sapiens.GRCh38.${params.ensembl_version}.chr.gtf` whereas STAR_FOR_ARRIBA uses `${params.ensembl_ref}/Homo_sapiens.GRCh38.${params.ensembl_version}.gtf`
    Output files @@ -451,13 +383,6 @@ For `STAR-fusion` with the parameters: - `.Aligned.out.bam` -**For squid:** - -- `.Aligned.sortedByCoord.out.bam` -- `.Chimeric.out.sam` -- `.unmapped_1.fastq.gz` -- `.unmapped_2.fastq.gz` - **For starfusion:** - `.Aligned.sortedByCoord.out.bam` diff --git a/docs/usage.md b/docs/usage.md index 9df6d24e..8b4fa8fd 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -13,7 +13,7 @@ The pipeline is divided into two parts: - required only once before running the pipeline - **Important**: has to be run with each new release 2. Detecting fusions - - Supported tools: `Arriba`, `FusionCatcher`, `pizzly`, `SQUID`, `STAR-Fusion`, and `StringTie` + - Supported tools: `Arriba`, `FusionCatcher`, `STAR-Fusion`, and `StringTie` - QC: `Fastqc`, `MultiQC`, and `Qualimap rnaseq` - Fusions visualization: `Arriba`, `fusion-report` and `FusionInspector`, VCF file creation based on `MegaFusion` @@ -123,7 +123,7 @@ As you can see above for multiple runs of the same sample, the `sample` name has ### Starting commands -The pipeline can either be run using all fusion detection tools or specifying individual tools. Visualisation tools will be run on all fusions detected. To run all tools (`arriba`, `fusioncatcher`, `pizzly`, `squid`, `starfusion`, `stringtie`) use the `--all` parameter: +The pipeline can either be run using all fusion detection tools or specifying individual tools. Visualisation tools will be run on all fusions detected. To run all tools (`arriba`, `fusioncatcher`, `starfusion`, `stringtie`) use the `--all` parameter: ```bash nextflow run nf-core/rnafusion \ @@ -299,9 +299,9 @@ There are two parameters to increase the `--limitSjdbInsertNsj` parameter if nec - `--fusioncatcher_limitSjdbInsertNsj`, default: 2000000 - `--fusioninspector_limitSjdbInsertNsj`, default: 1000000 -Use the parameter `--cram` to compress the BAM files to CRAM for specific tools. Options: arriba, squid, starfusion. Leave no space between options: +Use the parameter `--cram` to compress the BAM files to CRAM for specific tools. Options: arriba, starfusion. Leave no space between options: -- `--cram arriba,squid,starfusion`, default: [] +- `--cram arriba,starfusion`, default: [] - `--cram arriba` ### Updating the pipeline diff --git a/modules.json b/modules.json index 162a71b5..1e81bc7e 100644 --- a/modules.json +++ b/modules.json @@ -45,11 +45,6 @@ "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0", "installed_by": ["modules"] }, - "kallisto/index": { - "branch": "master", - "git_sha": "699fa6f3002d922380615f3847198aeb57d8b6a9", - "installed_by": ["modules"] - }, "multiqc": { "branch": "master", "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 38809803..0d674a7a 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -8,7 +8,7 @@ process FUSIONREPORT { input: - tuple val(meta), path(reads), path(arriba_fusions), path(pizzly_fusions), path(squid_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) + tuple val(meta), path(reads), path(arriba_fusions), path(starfusion_fusions), path(fusioncatcher_fusions) tuple val(meta2), path(fusionreport_ref) output: @@ -27,8 +27,6 @@ process FUSIONREPORT { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def tools = params.arriba || params.all ? "--arriba ${arriba_fusions} " : '' - tools += params.pizzly || params.all ? "--pizzly ${pizzly_fusions} " : '' - tools += params.squid || params.all ? "--squid ${squid_fusions} " : '' tools += params.starfusion || params.all ? "--starfusion ${starfusion_fusions} " : '' tools += params.fusioncatcher || params.all ? "--fusioncatcher ${fusioncatcher_fusions} " : '' def prefix = task.ext.prefix ?: "${meta.id}" diff --git a/modules/local/fusionreport/detect/meta.yml b/modules/local/fusionreport/detect/meta.yml index 7b9de84c..83ba76c7 100644 --- a/modules/local/fusionreport/detect/meta.yml +++ b/modules/local/fusionreport/detect/meta.yml @@ -24,14 +24,6 @@ input: type: path description: File pattern: "*.fusions.tsv" - - pizzly_fusions: - type: path - description: File containing fusions from pizzly - pattern: "*.pizzly.txt" - - squid_fusions: - type: path - description: File containing fusions from squid - pattern: "*.annotated.txt" - starfusion_fusions: type: path description: File containing fusions from STARfusion diff --git a/modules/local/kallisto/quant/main.nf b/modules/local/kallisto/quant/main.nf deleted file mode 100644 index 7d3e5dfb..00000000 --- a/modules/local/kallisto/quant/main.nf +++ /dev/null @@ -1,47 +0,0 @@ -process KALLISTO_QUANT { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::kallisto=0.46.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - 'quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1' }" - - - input: - tuple val(meta), path(reads) - path index - - output: - path "versions.yml" , emit: versions - tuple val(meta), path("*fusions.txt") , emit: txt - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - kallisto quant \ - -t $task.cpus \ - -i $index \ - --fusion \ - -o . \ - $reads - mv fusion.txt ${prefix}.kallisto_quant.fusions.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.kallisto_quant.fusions.txt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS - """ -} - diff --git a/modules/local/kallisto/quant/meta.yml b/modules/local/kallisto/quant/meta.yml deleted file mode 100644 index 31821aa6..00000000 --- a/modules/local/kallisto/quant/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: kallisto_quant -description: runs the kallisto quantification algorithm - - quant -tools: - - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. - homepage: https://pachterlab.github.io/kallisto/ - documentation: https://pachterlab.github.io/kallisto/manual - tool_dev_url: https://github.com/pachterlab/kallisto - doi: "" - licence: ["BSD-2-Clause"] - -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file - pattern: "*.{fastq}" - - reference: - type: directory - description: Path to kallisto index - pattern: "*" - -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fusions: - type: file - description: fusions - pattern: "*.txt" - -authors: - - "@rannick" diff --git a/modules/local/pizzly/detect/main.nf b/modules/local/pizzly/detect/main.nf deleted file mode 100644 index a610b531..00000000 --- a/modules/local/pizzly/detect/main.nf +++ /dev/null @@ -1,49 +0,0 @@ -process PIZZLY { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::kallisto=0.46.2 bioconda::pizzly==0.37.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pizzly:0.37.3--py36_2' : - 'quay.io/biocontainers/pizzly:0.37.3--h470a237_3' }" - - input: - tuple val(meta), path(txt) - tuple val(meta2), path(transcript) - tuple val(meta3), path(gtf) - - output: - path "versions.yml" , emit: versions - tuple val(meta), path("*pizzly.txt") , emit: fusions - tuple val(meta), path("*unfiltered.json") , emit: fusions_unfiltered - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - pizzly \\ - $args \\ - --gtf $gtf \\ - --fasta $transcript \\ - --output ${prefix}.pizzly $txt - - pizzly_flatten_json.py ${prefix}.pizzly.json ${prefix}.pizzly.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pizzly: \$(pizzly --version | grep pizzly | sed -e "s/pizzly version: //g") - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.pizzly.txt - touch ${prefix}.pizzly.unfiltered.json - cat <<-END_VERSIONS > versions.yml - "${task.process}": - pizzly: \$(pizzly --version | grep pizzly | sed -e "s/pizzly version: //g") - END_VERSIONS - """ -} - diff --git a/modules/local/pizzly/detect/meta.yml b/modules/local/pizzly/detect/meta.yml deleted file mode 100644 index 930b3a62..00000000 --- a/modules/local/pizzly/detect/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: pizzly -description: Pizzly detection of fusions. -keywords: - - fusion - - pizzly -tools: - - pizzly: - description: Fast fusion detection using kallisto - homepage: https://github.com/pmelsted/pizzly - documentation: https://github.com/pmelsted/pizzly - tool_dev_url: https://github.com/pmelsted/pizzly - doi: "" - licence: ["BSD-2-Clause"] - -input: - - fasta: - type: file - description: genome fasta file - pattern: "*.{fasta*}" - - reference: - type: directory - description: Path to kallisto index - pattern: "*" - - gtf: - type: file - description: gtf reference - pattern: "*.gtf" - -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fusions: - type: file - description: fusions - pattern: "*pizzly.txt" - - unfiltered: - type: file - description: unfiltered fusions - pattern: "*unfiltered.json" - -authors: - - "@rannick" diff --git a/modules/local/pizzly/download/main.nf b/modules/local/pizzly/download/main.nf deleted file mode 100644 index efaae3aa..00000000 --- a/modules/local/pizzly/download/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -process PIZZLY_DOWNLOAD { - tag "pizzly" - label 'process_medium' - - conda "bioconda::kallisto=0.46.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - 'quay.io/biocontainers/kallisto:0.46.2--h4f7b962_1' }" - - input: - tuple val(meta), path(transcript) - - output: - path "versions.yml" , emit: versions - path "index.idx" , emit: reference - - script: - def args = task.ext.args ?: '' - """ - kallisto index \\ - -i index.idx \\ - $args \\ - $transcript - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS """ - - stub: - """ - touch index.idx - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS - """ - -} diff --git a/modules/local/squid/annotate/main.nf b/modules/local/squid/annotate/main.nf deleted file mode 100644 index 9b6eebe7..00000000 --- a/modules/local/squid/annotate/main.nf +++ /dev/null @@ -1,41 +0,0 @@ - -process SQUID_ANNOTATE { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::squid=1.5" - container "docker.io/nfcore/rnafusion:squid_1.5-star2.7.1a" - - - - input: - tuple val(meta), path(txt) - tuple val(meta2), path(gtf) - - output: - tuple val(meta), path("*annotated.txt") , emit: fusions_annotated - path "versions.yml" , emit: versions - - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - AnnotateSQUIDOutput.py $gtf $txt ${prefix}.squid.fusions.annotated.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - squid: \$(echo \$(squid --version 2>&1) | sed 's/v//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.squid.fusions.annotated.txt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - squid: \$(echo \$(squid --version 2>&1) | sed 's/v//') - END_VERSIONS - """ -} diff --git a/modules/local/squid/annotate/meta.yml b/modules/local/squid/annotate/meta.yml deleted file mode 100644 index e1a1f0d2..00000000 --- a/modules/local/squid/annotate/meta.yml +++ /dev/null @@ -1,36 +0,0 @@ -name: squid -description: Squid detection of fusions. -keywords: - - fusion - - pizzly -tools: - - pizzly: - description: Fusion detection using squid - homepage: https://github.com/Kingsford-Group/squid - documentation: https://github.com/Kingsford-Group/squid - tool_dev_url: https://github.com/Kingsford-Group/squid - doi: "" - licence: ["BSD-3-Clause"] - -input: - - fusions: - type: directory - description: Path to squid fusions - pattern: "*.txt" - - gtf: - type: file - description: gtf reference - pattern: "*.gtf" - -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fusions_annotated: - type: file - description: squid fusions annotated - pattern: "*squid.fusions.annotated.txt" - -authors: - - "@rannick" diff --git a/modules/local/squid/detect/main.nf b/modules/local/squid/detect/main.nf deleted file mode 100644 index 3ccb6e3e..00000000 --- a/modules/local/squid/detect/main.nf +++ /dev/null @@ -1,40 +0,0 @@ - -process SQUID { - tag "squid" - label 'process_medium' - - conda "bioconda::squid=1.5" - container "docker.io/nfcore/rnafusion:squid_1.5-star2.7.1a" - - - - input: - tuple val(meta), path(bam), path(chimeric_bam) - - output: - tuple val(meta), path("*sv.txt") , emit: fusions - path "versions.yml" , emit: versions - - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - """ - squid -b $bam -c $chimeric_bam -o ${prefix}.squid.fusions - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - squid: \$(echo \$(squid --version 2>&1) | sed 's/v//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.squid.fusions_sv.txt - cat <<-END_VERSIONS > versions.yml - "${task.process}": - squid: \$(echo \$(squid --version 2>&1) | sed 's/v//') - END_VERSIONS - """ -} diff --git a/modules/local/squid/detect/meta.yml b/modules/local/squid/detect/meta.yml deleted file mode 100644 index a7f1e61a..00000000 --- a/modules/local/squid/detect/meta.yml +++ /dev/null @@ -1,41 +0,0 @@ -name: squid -description: Squid detection of fusions. -keywords: - - fusion - - pizzly -tools: - - pizzly: - description: Fusion detection using squid - homepage: https://github.com/Kingsford-Group/squid - documentation: https://github.com/Kingsford-Group/squid - tool_dev_url: https://github.com/Kingsford-Group/squid - doi: "" - licence: ["BSD-3-Clause"] - -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - chimeric_bam: - type: file - description: BAM/CRAM/SAM file containing only chimeric sorted reads - pattern: "*.{bam,cram,sam}" - -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fusions: - type: directory - description: Path to squid fusions - pattern: "*.txt" - -authors: - - "@rannick" diff --git a/modules/nf-core/kallisto/index/main.nf b/modules/nf-core/kallisto/index/main.nf deleted file mode 100644 index fb9e44d9..00000000 --- a/modules/nf-core/kallisto/index/main.nf +++ /dev/null @@ -1,44 +0,0 @@ -process KALLISTO_INDEX { - tag "$fasta" - label 'process_medium' - - conda "bioconda::kallisto=0.46.2" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kallisto:0.46.2--h4f7b962_1' : - 'biocontainers/kallisto:0.46.2--h4f7b962_1' }" - - input: - tuple val(meta), path(fasta) - - output: - tuple val(meta), path("kallisto") , emit: index - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - """ - kallisto \\ - index \\ - $args \\ - -i kallisto \\ - $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS - """ - - stub: - """ - touch kallisto - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - kallisto: \$(echo \$(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml deleted file mode 100644 index 05dfa53d..00000000 --- a/modules/nf-core/kallisto/index/meta.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: kallisto_index -description: Create kallisto index -keywords: - - kallisto - - kallisto/index - - index -tools: - - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. - homepage: https://pachterlab.github.io/kallisto/ - documentation: https://pachterlab.github.io/kallisto/manual - tool_dev_url: https://github.com/pachterlab/kallisto - - licence: ["BSD-2-Clause"] - -input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: genome fasta file - pattern: "*.{fasta}" - -output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: - type: directory - description: Kallisto genome index - pattern: "*.idx" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - -authors: - - "@ggabernet" diff --git a/nextflow.config b/nextflow.config index 994e96e3..4f8330f8 100644 --- a/nextflow.config +++ b/nextflow.config @@ -55,8 +55,6 @@ params { all = false arriba = false fusioncatcher = false - pizzly = false - squid = false starindex = false starfusion = false stringtie = false @@ -75,8 +73,6 @@ params { arriba_ref_known_fusions = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz" arriba_ref_protein_domains = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3" fusioncatcher_ref = "${params.genomes_base}/fusioncatcher/human_v102" - pizzly_ref = "${params.genomes_base}/pizzly/kallisto" - squid_ref = "${params.genomes_base}/squid" starfusion_ref = "${params.genomes_base}/starfusion/ctat_genome_lib_build_dir" starindex_ref = "${params.genomes_base}/star" fusionreport_ref = "${params.genomes_base}/fusion_report_db" @@ -84,8 +80,6 @@ params { // Path to fusion outputs arriba_fusions = null - pizzly_fusions = null - squid_fusions = null starfusion_fusions = null fusioncatcher_fusions = null fusioninspector_fusions = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 02cd1e27..b8ed5d97 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -185,36 +185,6 @@ "default": true, "description": "Display fusions identified with 2 tools or more" }, - "pizzly": { - "type": "boolean", - "fa_icon": "far fa-file-code", - "description": "Build or run pizzly references/analyses" - }, - "pizzly_fusions": { - "type": "string", - "fa_icon": "far fa-file-code", - "description": "Path to pizzly output" - }, - "pizzly_ref": { - "type": "string", - "fa_icon": "far fa-file-code", - "description": "Path to pizzly references" - }, - "squid": { - "type": "boolean", - "fa_icon": "far fa-file-code", - "description": "Build or run squid references/analyses" - }, - "squid_fusions": { - "type": "string", - "fa_icon": "far fa-file-code", - "description": "Path to squid output" - }, - "squid_ref": { - "type": "string", - "fa_icon": "far fa-file-code", - "description": "Path to squid references" - }, "starfusion": { "type": "boolean", "fa_icon": "far fa-file-code", @@ -303,7 +273,7 @@ "properties": { "cram": { "type": "string", - "description": "List of tools for which to compress BAM file to CRAM,default: [], options: arriba, squid, starfusion. Leave no space between options", + "description": "List of tools for which to compress BAM file to CRAM,default: [], options: arriba, starfusion. Leave no space between options", "fa_icon": "fas fa-cut" } } diff --git a/subworkflows/local/fusionreport_workflow.nf b/subworkflows/local/fusionreport_workflow.nf index 478986a4..25238e1b 100644 --- a/subworkflows/local/fusionreport_workflow.nf +++ b/subworkflows/local/fusionreport_workflow.nf @@ -6,8 +6,6 @@ workflow FUSIONREPORT_WORKFLOW { reads fusionreport_ref arriba_fusions - pizzly_fusions - squid_fusions starfusion_fusions fusioncatcher_fusions @@ -18,8 +16,6 @@ workflow FUSIONREPORT_WORKFLOW { if (!params.fusioninspector_only) { reads_fusions = reads .join(arriba_fusions, remainder: true) - .join(pizzly_fusions, remainder: true) - .join(squid_fusions, remainder: true) .join(starfusion_fusions, remainder: true) .join(fusioncatcher_fusions, remainder: true) diff --git a/subworkflows/local/pizzly_workflow.nf b/subworkflows/local/pizzly_workflow.nf deleted file mode 100644 index 7675432b..00000000 --- a/subworkflows/local/pizzly_workflow.nf +++ /dev/null @@ -1,37 +0,0 @@ -include { KALLISTO_QUANT } from '../../modules/local/kallisto/quant/main' -include { PIZZLY } from '../../modules/local/pizzly/detect/main' - -workflow PIZZLY_WORKFLOW { - take: - reads - ch_gtf - ch_transcript - - main: - ch_versions = Channel.empty() - ch_dummy_file = file("$baseDir/assets/dummy_file_pizzly.txt", checkIfExists: true) - - if ((params.pizzly || params.all) && !params.fusioninspector_only) { - if (params.pizzly_fusions) { - ch_pizzly_fusions = reads.combine(Channel.value(file(params.pizzly_fusions, checkIfExists:true))) - .map { meta, reads, fusions -> [ meta, fusions ] } - } else { - KALLISTO_QUANT(reads, params.pizzly_ref ) - ch_versions = ch_versions.mix(KALLISTO_QUANT.out.versions) - - PIZZLY( KALLISTO_QUANT.out.txt, ch_transcript, ch_gtf ) - ch_versions = ch_versions.mix(PIZZLY.out.versions) - - ch_pizzly_fusions = PIZZLY.out.fusions - } - } - else { - ch_pizzly_fusions = reads.combine(Channel.value(file(ch_dummy_file, checkIfExists:true))) - .map { meta, reads, fusions -> [ meta, fusions ] } - } - - emit: - fusions = ch_pizzly_fusions - versions = ch_versions.ifEmpty(null) - } - diff --git a/subworkflows/local/squid_workflow.nf b/subworkflows/local/squid_workflow.nf deleted file mode 100644 index c4f29425..00000000 --- a/subworkflows/local/squid_workflow.nf +++ /dev/null @@ -1,80 +0,0 @@ -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_SQUID } from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_FOR_SQUID_CHIMERIC } from '../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_FOR_SQUID_CHIMERIC } from '../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_SQUID_CHIMERIC } from '../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_SQUID_CRAM } from '../../modules/nf-core/samtools/view/main' -include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_FOR_SQUID_CRAM_CHIMERIC } from '../../modules/nf-core/samtools/view/main' -include { SQUID } from '../../modules/local/squid/detect/main' -include { SQUID_ANNOTATE } from '../../modules/local/squid/annotate/main' -include { STAR_ALIGN as STAR_FOR_SQUID } from '../../modules/nf-core/star/align/main' - -workflow SQUID_WORKFLOW { - - take: - reads - ch_gtf - ch_starindex_ensembl_ref - ch_fasta - - main: - ch_versions = Channel.empty() - ch_dummy_file = file("$baseDir/assets/dummy_file_squid.txt", checkIfExists: true) - - if ((params.squid || params.all) && !params.fusioninspector_only) { - if (params.squid_fusions){ - ch_squid_fusions = reads.combine(Channel.value(file(params.squid_fusions, checkIfExists:true))) - .map { meta, reads, fusions -> [ meta, fusions ] } - } else { - - STAR_FOR_SQUID(reads, ch_starindex_ensembl_ref, ch_gtf, params.star_ignore_sjdbgtf, '', params.seq_center ?: '') - ch_versions = ch_versions.mix(STAR_FOR_SQUID.out.versions) - - STAR_FOR_SQUID.out.sam - .map { meta, sam -> - return [meta, sam, []] - }.set { chimeric_sam } - - - - SAMTOOLS_VIEW_FOR_SQUID_CHIMERIC (chimeric_sam, ch_fasta, []) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_SQUID_CHIMERIC.out.versions) - - SAMTOOLS_SORT_FOR_SQUID_CHIMERIC (SAMTOOLS_VIEW_FOR_SQUID_CHIMERIC.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_SQUID_CHIMERIC.out.versions) - - bam_chimeric = STAR_FOR_SQUID.out.bam_sorted.join(SAMTOOLS_SORT_FOR_SQUID_CHIMERIC.out.bam) - - if (params.cram.contains('squid')){ - SAMTOOLS_INDEX_FOR_SQUID(STAR_FOR_SQUID.out.bam_sorted) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_SQUID.out.versions) - SAMTOOLS_INDEX_FOR_SQUID_CHIMERIC(SAMTOOLS_SORT_FOR_SQUID_CHIMERIC.out.bam) - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_FOR_SQUID_CHIMERIC.out.versions) - - bam_sorted_indexed = STAR_FOR_SQUID.out.bam_sorted.join(SAMTOOLS_INDEX_FOR_SQUID.out.bai) - chimeric_sorted_indexed = SAMTOOLS_SORT_FOR_SQUID_CHIMERIC.out.bam.join(SAMTOOLS_INDEX_FOR_SQUID_CHIMERIC.out.bai) - - SAMTOOLS_VIEW_FOR_SQUID_CRAM (bam_sorted_indexed, ch_fasta, []) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_SQUID_CRAM.out.versions) - SAMTOOLS_VIEW_FOR_SQUID_CRAM_CHIMERIC (chimeric_sorted_indexed, ch_fasta, []) - ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_SQUID_CRAM.out.versions) - } - - SQUID (bam_chimeric) - ch_versions = ch_versions.mix(SQUID.out.versions) - - SQUID_ANNOTATE (SQUID.out.fusions, ch_gtf) - ch_versions = ch_versions.mix(SQUID_ANNOTATE.out.versions) - - ch_squid_fusions = SQUID_ANNOTATE.out.fusions_annotated - } - } - else { - ch_squid_fusions = reads.combine(Channel.value(file(ch_dummy_file, checkIfExists:true))) - .map { meta, reads, fusions -> [ meta, fusions ] } - } - - emit: - fusions = ch_squid_fusions - versions = ch_versions.ifEmpty(null) - } - diff --git a/tower.yml b/tower.yml index 5813f5d3..1aa32e24 100644 --- a/tower.yml +++ b/tower.yml @@ -19,14 +19,10 @@ reports: display: "Picard: Metrics from CollectRnaMetrics" "**/picard/*_rna_metrics.txt": display: "Picard: Metrics from MarkDuplicates" - "**/pizzly/*.pizzly.txt": - display: "Pizzly identified fusion TXT report" "**/qualimap/qualimapReport.html": display: "Qualimap HTML report from STAR_FOR_STARFUSION alignment" "**/qualimap/rnaseq_qc_results.txt": display: "Qualimap QC results from STAR_FOR_STARFUSION alignment in TXT format" - "**/squid/*.squid.fusions.annotated.txt": - display: "Squid identified fusion TXT report" "**/star_for_starfusion/*ReadsPerGene.out.tab": display: "Number of reads per gene" "**/starfusion/*.starfusion.fusion_predictions.tsv": diff --git a/workflows/build_references.nf b/workflows/build_references.nf index 6a03edb6..4921443a 100644 --- a/workflows/build_references.nf +++ b/workflows/build_references.nf @@ -21,7 +21,6 @@ include { CONVERT2BED } from '../modules/local/convert2bed/m include { SAMTOOLS_FAIDX } from '../modules/nf-core/samtools/faidx/main' include { STAR_GENOMEGENERATE } from '../modules/nf-core/star/genomegenerate/main' -include { KALLISTO_INDEX as PIZZLY_INDEX } from '../modules/nf-core/kallisto/index/main' include { GATK4_CREATESEQUENCEDICTIONARY } from '../modules/nf-core/gatk4/createsequencedictionary/main' include { GATK4_BEDTOINTERVALLIST } from '../modules/nf-core/gatk4/bedtointervallist/main' @@ -47,7 +46,7 @@ workflow BUILD_REFERENCES { GATK4_BEDTOINTERVALLIST(CONVERT2BED.out.bed, GATK4_CREATESEQUENCEDICTIONARY.out.dict) - if (params.starindex || params.all || params.starfusion || params.arriba || params.squid ) { + if (params.starindex || params.all || params.starfusion || params.arriba) { STAR_GENOMEGENERATE( ENSEMBL_DOWNLOAD.out.fasta, ENSEMBL_DOWNLOAD.out.gtf ) } @@ -59,10 +58,6 @@ workflow BUILD_REFERENCES { FUSIONCATCHER_DOWNLOAD() } - if (params.pizzly || params.all) { - PIZZLY_INDEX( ENSEMBL_DOWNLOAD.out.transcript ) - } - if (params.starfusion || params.all) { if (params.starfusion_build){ STARFUSION_BUILD( ENSEMBL_DOWNLOAD.out.fasta, ENSEMBL_DOWNLOAD.out.chrgtf ) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 6f498e11..8783570b 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -54,7 +54,6 @@ if (params_fasta_path_uri){ else { for (param in checkPathParamList) if ((param.toString())!= file(param).toString() && !params.build_references) { exit 1, "Problem with ${param}: ABSOLUTE PATHS are required! Check for trailing '/' at the end of paths too." } } -if ((params.squid || params.all) && params.ensembl_version != 102) { exit 1, 'Ensembl version is not supported by squid' } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -80,9 +79,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil include { INPUT_CHECK } from '../subworkflows/local/input_check' include { TRIM_WORKFLOW } from '../subworkflows/local/trim_workflow' include { ARRIBA_WORKFLOW } from '../subworkflows/local/arriba_workflow' -include { PIZZLY_WORKFLOW } from '../subworkflows/local/pizzly_workflow' include { QC_WORKFLOW } from '../subworkflows/local/qc_workflow' -include { SQUID_WORKFLOW } from '../subworkflows/local/squid_workflow' include { STARFUSION_WORKFLOW } from '../subworkflows/local/starfusion_workflow' include { STRINGTIE_WORKFLOW } from '../subworkflows/local/stringtie_workflow' include { FUSIONCATCHER_WORKFLOW } from '../subworkflows/local/fusioncatcher_workflow' @@ -180,26 +177,6 @@ workflow RNAFUSION { ) ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions.first().ifEmpty(null)) - // Run pizzly/kallisto - - PIZZLY_WORKFLOW ( - ch_reads_all, - ch_gtf, - ch_transcript - ) - ch_versions = ch_versions.mix(PIZZLY_WORKFLOW.out.versions.first().ifEmpty(null)) - - -// Run squid - - SQUID_WORKFLOW ( - ch_reads_all, - ch_gtf, - ch_starindex_ensembl_ref, - ch_fasta - ) - ch_versions = ch_versions.mix(SQUID_WORKFLOW.out.versions.first().ifEmpty(null)) - //Run STAR fusion STARFUSION_WORKFLOW ( @@ -231,8 +208,6 @@ workflow RNAFUSION { ch_reads_all, ch_fusionreport_ref, ARRIBA_WORKFLOW.out.fusions, - PIZZLY_WORKFLOW.out.fusions, - SQUID_WORKFLOW.out.fusions, STARFUSION_WORKFLOW.out.fusions, FUSIONCATCHER_WORKFLOW.out.fusions ) From 0535880964c4ab0c1e555e1d177cde57db5b7866 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 25 Sep 2023 10:39:32 +0200 Subject: [PATCH 094/264] bump version to 3.0.0 --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5e0f10e0..44a9684d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-rnafusion-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 994e96e3..909edafe 100644 --- a/nextflow.config +++ b/nextflow.config @@ -295,7 +295,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.4.0' + version = '3.0.0dev' doi = '' } From 889df95f80ec8993e17d28cb5070ea92206d253e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 25 Sep 2023 13:25:00 +0200 Subject: [PATCH 095/264] update modules.config --- conf/modules.config | 73 ++------------------------------------------- 1 file changed, 3 insertions(+), 70 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b4dc96d6..51d41ce2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -133,14 +133,6 @@ process { ] } - withName: KALLISTO_INDEX { - ext.args = '-k 31' - publishDir = [ - path: { "${params.genomes_base}/pizzly" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - } withName: MEGAFUSION { ext.when = {!params.fusioninspector_only} ext.prefix = { "${meta.id}_fusion_data" } @@ -157,20 +149,16 @@ process { } - withName: PICARD_MARKDUPLICATES { + withName: GATK4_MARKDUPLICATES { ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) } - } - - withName: PIZZLY { - ext.args = "-k 31 --align-score 2 --insert-size 400 --cache index.cache.txt" publishDir = [ - path: { "${params.outdir}/pizzly" }, + path: { "${params.outdir}/picard" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, ] } - withName: QUALIMAP_RNASEQ { + withName: MOSDEPTH { ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)} } @@ -203,15 +191,6 @@ process { ] } - withName: SAMTOOLS_SORT_FOR_SQUID_CHIMERIC { - ext.prefix = { "${meta.id}_chimeric_sorted" } - publishDir = [ - path: { "${params.outdir}/samtools_sort_for_squid_chimeric" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: SAMTOOLS_VIEW_FOR_ARRIBA { ext.args = { "--output-fmt cram" } ext.prefix = { "${meta.id}_star_for_arriba" } @@ -222,35 +201,6 @@ process { ] } - withName: SAMTOOLS_VIEW_FOR_SQUID_CHIMERIC { - ext.prefix = { "${meta.id}_chimeric" } - ext.args = { "--output-fmt bam" } - publishDir = [ - path: { "${params.outdir}/samtools_view_for_squid_chimeric" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM { - ext.args = { "--output-fmt cram" } - publishDir = [ - path: { "${params.outdir}/cram_squid" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SAMTOOLS_VIEW_FOR_SQUID_CRAM_CHIMERIC { - ext.args = { "--output-fmt cram" } - ext.prefix = { "${meta.id}_chimeric" } - publishDir = [ - path: { "${params.outdir}/cram_squid" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - withName: SAMTOOLS_VIEW_FOR_STARFUSION { ext.args = { "--output-fmt cram" } ext.prefix = { "${meta.id}.star_for_starfusion.Aligned.sortedByCoord.out" } @@ -285,23 +235,6 @@ process { --chimMultimapNmax 50' } - withName: STAR_FOR_SQUID { - publishDir = [ - path: { "${params.outdir}/star_for_squid" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - ext.args = '--twopassMode Basic \ - --chimOutType SeparateSAMold \ - --chimSegmentMin 20 \ - --chimJunctionOverhangMin 12 \ - --alignSJDBoverhangMin 10 \ - --outReadsUnmapped Fastx \ - --outSAMstrandField intronMotif \ - --outSAMtype BAM SortedByCoordinate \ - --readFilesCommand zcat' - } - withName: STAR_FOR_STARFUSION { publishDir = [ path: { "${params.outdir}/star_for_starfusion" }, From f7fe23ad6306ed955e7144b0911e690491d96902 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 25 Sep 2023 13:27:16 +0200 Subject: [PATCH 096/264] update changelog --- CHANGELOG.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c9ff036..17be2667 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v3.0.0dev + +### Added + +### Changed + +- Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389) + +### Fixed + +### Removed + ## v2.4.0 - [2023/09/22] ### Added From 80b634718eb55585a4c51336e9168b5f9661bffd Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 25 Sep 2023 13:39:59 +0200 Subject: [PATCH 097/264] prettify --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b54f6e2c..c933176d 100644 --- a/README.md +++ b/README.md @@ -48,9 +48,9 @@ In rnafusion the full-sized test includes reference building and fusion detectio 7. Fusioncatcher subworkflow - [FusionCatcher](https://github.com/ndaniel/fusioncatcher) fusion detection 8. StringTie subworkflow - - [StringTie](https://ccb.jhu.edu/software/stringtie/) + - [StringTie](https://ccb.jhu.edu/software/stringtie/) 9. Fusion-report - - Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) + - Merge all fusions detected by the selected tools with [Fusion-report](https://github.com/Clinical-Genomics/fusion-report) 10. Post-processing and analysis of data - [FusionInspector](https://github.com/FusionInspector/FusionInspector) - [Arriba](https://github.com/suhrig/arriba) visualisation From 318733163ee60b96deab16194d973c597f0dd310 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 26 Sep 2023 08:09:03 +0000 Subject: [PATCH 098/264] Template update for nf-core/tools version 2.10 --- .devcontainer/devcontainer.json | 1 + .github/CONTRIBUTING.md | 4 +- .github/workflows/linting.yml | 2 +- .github/workflows/release-announcments.yml | 68 +++++++++ CHANGELOG.md | 2 +- CITATIONS.md | 2 +- CODE_OF_CONDUCT.md | 133 ++++++++++++++---- README.md | 21 +-- assets/multiqc_config.yml | 4 +- conf/modules.config | 9 ++ docs/output.md | 5 +- docs/usage.md | 16 ++- lib/NfcoreTemplate.groovy | 16 +++ lib/WorkflowRnafusion.groovy | 2 +- main.nf | 3 + modules.json | 6 +- .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/main.nf | 8 +- modules/nf-core/multiqc/main.nf | 2 +- nextflow.config | 9 +- nextflow_schema.json | 15 -- workflows/rnafusion.nf | 1 + 22 files changed, 253 insertions(+), 78 deletions(-) create mode 100644 .github/workflows/release-announcments.yml diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a584..4ecfbfe3 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 975df6cd..5e32dfd8 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +9,9 @@ Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! Contributions to the code are even more welcome ;) -> If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/rnafusion then the best place to ask is on the nf-core Slack [#rnafusion](https://nfcore.slack.com/channels/rnafusion) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4bc..b8bdd214 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -78,7 +78,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 00000000..6ad33927 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/CHANGELOG.md b/CHANGELOG.md index 5470be26..d09f1be9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v2.3.4 - [date] +## v3.0.0dev - [date] Initial release of nf-core/rnafusion, created with the [nf-core](https://nf-co.re/) template. diff --git a/CITATIONS.md b/CITATIONS.md index 1d65b743..98bdbc60 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,7 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. + > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052f..c089ec78 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/README.md b/README.md index 504929dd..b4605ebd 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # ![nf-core/rnafusion](docs/images/nf-core-rnafusion_logo_light.png#gh-light-mode-only) ![nf-core/rnafusion](docs/images/nf-core-rnafusion_logo_dark.png#gh-dark-mode-only) -[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnafusion/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -29,10 +30,11 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +:::note +If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how +to set-up Nextflow. 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Qualimap - MultiQC FusionInspector + x="220.19096" + y="96.223259">FusionInspector fusion-report + x="196.76082" + y="64.750114">fusion-report PicardPicard:CollectRnaSeqMetrics- CollectRnaSeqMetrics+- CollectWgsMetricsPicardCollectWgsMetrics - SQUIDannotate + id="tspan23187">- CollectInsertSizeMetrics - - - - + style="fill:none;stroke:#000000;stroke-width:2.42956;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1" + d="m 261.03273,71.013135 h -7.93593 c -3.94345,0 -7.79288,2.347188 -10.58131,4.962803 l -2.64532,2.481411" + id="path1232-7-2-7-3-7" + sodipodi:nodetypes="cssc" /> + + transform="translate(-10.236147,12.330532)"> qc Workflows: - - StringTie - + transform="translate(-9.762502,12.377831)"> - + sodipodi:nodetypes="ccc" /> squid - pizzly - stringtie - + y="147.22173">stringtie ArribaArribavisualisation + VCFcollect + + From 6fee33a833fb84bb5d6ebe2d0bcd4cffb375738c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 1 Nov 2023 11:55:01 +0100 Subject: [PATCH 170/264] fix typo --- subworkflows/local/arriba_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index c4827407..3aa9c090 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -40,7 +40,7 @@ workflow ARRIBA_WORKFLOW { SAMTOOLS_SORT_FOR_ARRIBA(STAR_FOR_ARRIBA.out.bam) ch_versions = ch_versions.mix(SAMTOOLS_SORT_FOR_ARRIBA.out.versions ) - SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, []) + SAMTOOLS_VIEW_FOR_ARRIBA(SAMTOOLS_SORT_FOR_ARRIBA.out.bam.map { meta, bam -> [ meta, bam, [] ] }, ch_fasta, []) ch_versions = ch_versions.mix(SAMTOOLS_VIEW_FOR_ARRIBA.out.versions ) SAMTOOLS_INDEX_FOR_ARRIBA(SAMTOOLS_VIEW_FOR_ARRIBA.out.cram) From 0b67a98b52decd09df5a3a05c0c69b5d25d56516 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 1 Nov 2023 12:09:47 +0100 Subject: [PATCH 171/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3085346e..912ba695 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added - Add picard CollectInserSizeMetrics to QC workflow [#408](https://github.com/nf-core/rnafusion/pull/408) +- Build CRAM index in the same directory as CRAM files for arriba and STAR-Fusion [#427](https://github.com/nf-core/rnafusion/pull/427) ### Changed From a9bfa7d634c60543931d52b431471e10307219d4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 1 Nov 2023 14:34:10 +0100 Subject: [PATCH 172/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c9ff036..d56c52d1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - cram file from output bam of `STAR_FOR_STARFUSION`: meta.id to meta.id.star_for_starfusion.Aligned.sortedByCoord.out - `fusion-report` index.html file to meta.id_fusionreport_index.html - meta.id.vcf output from `MEGAFUSION` to meta.id_fusion_data.vcf + - Update metro map [#428](https://github.com/nf-core/rnafusion/pull/428) ### Fixed From cc4ec30388dce42bdb7fd8ac1bbdbe1caf558f94 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:20:04 +0100 Subject: [PATCH 173/264] install agat/convertspgff2tsv from nf-core --- modules.json | 5 ++ .../agat/convertspgff2tsv/environment.yml | 6 ++ modules/nf-core/agat/convertspgff2tsv/main.nf | 35 +++++++++ .../nf-core/agat/convertspgff2tsv/meta.yml | 38 ++++++++++ modules/nf-core/picard/markduplicates/main.nf | 65 +++++++++++++++++ .../nf-core/picard/markduplicates/meta.yml | 71 +++++++++++++++++++ .../execution_trace_2023-11-01_15-05-02.txt | 1 + 7 files changed, 221 insertions(+) create mode 100644 modules/nf-core/agat/convertspgff2tsv/environment.yml create mode 100644 modules/nf-core/agat/convertspgff2tsv/main.nf create mode 100644 modules/nf-core/agat/convertspgff2tsv/meta.yml create mode 100644 modules/nf-core/picard/markduplicates/main.nf create mode 100644 modules/nf-core/picard/markduplicates/meta.yml create mode 100644 null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt diff --git a/modules.json b/modules.json index 9805e2ef..beb0e954 100644 --- a/modules.json +++ b/modules.json @@ -5,6 +5,11 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "agat/convertspgff2tsv": { + "branch": "master", + "git_sha": "53e6fd5d80141e00a3b70762f4361f6af1f4303b", + "installed_by": ["modules"] + }, "arriba": { "branch": "master", "git_sha": "ea9e2892a9d12e8769402f12096219942bcf6536", diff --git a/modules/nf-core/agat/convertspgff2tsv/environment.yml b/modules/nf-core/agat/convertspgff2tsv/environment.yml new file mode 100644 index 00000000..9ca0ea28 --- /dev/null +++ b/modules/nf-core/agat/convertspgff2tsv/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::agat=1.2.0 diff --git a/modules/nf-core/agat/convertspgff2tsv/main.nf b/modules/nf-core/agat/convertspgff2tsv/main.nf new file mode 100644 index 00000000..cef48360 --- /dev/null +++ b/modules/nf-core/agat/convertspgff2tsv/main.nf @@ -0,0 +1,35 @@ +process AGAT_CONVERTSPGFF2TSV { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/agat:1.2.0--pl5321hdfd78af_0' : + 'biocontainers/agat:1.2.0--pl5321hdfd78af_0' }" + + input: + tuple val(meta), path(gff) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + agat_convert_sp_gff2tsv.pl \\ + --gff $gff \\ + --output ${prefix}.tsv \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + agat: \$(agat_convert_sp_gff2tsv.pl --help | sed '3!d; s/.*v//' | sed 's/ .*//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/agat/convertspgff2tsv/meta.yml b/modules/nf-core/agat/convertspgff2tsv/meta.yml new file mode 100644 index 00000000..f5865dfe --- /dev/null +++ b/modules/nf-core/agat/convertspgff2tsv/meta.yml @@ -0,0 +1,38 @@ +name: agat_convertspgff2tsv +description: | + Converts a GFF/GTF file into a TSV file +keywords: + - genome + - gff + - gtf + - conversion + - tsv +tools: + - agat: + description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + homepage: "https://github.com/NBISweden/AGAT" + documentation: "https://agat.readthedocs.io/" + tool_dev_url: "https://github.com/NBISweden/AGAT" + doi: "10.5281/zenodo.3552717" + licence: ["GPL v3"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" +output: + - tsv: + type: file + description: Annotation file in TSV format + pattern: "*.{gtf}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@rannick" diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf new file mode 100644 index 00000000..ebfa0864 --- /dev/null +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -0,0 +1,65 @@ +process PICARD_MARKDUPLICATES { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::picard=3.0.0" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : + 'biocontainers/picard:3.0.0--hdfd78af_1' }" + + input: + tuple val(meta), path(bam) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + + output: + tuple val(meta), path("*.bam") , emit: bam + tuple val(meta), path("*.bai") , optional:true, emit: bai + tuple val(meta), path("*.metrics.txt"), emit: metrics + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def avail_mem = 3072 + if (!task.memory) { + log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + + """ + picard \\ + -Xmx${avail_mem}M \\ + MarkDuplicates \\ + $args \\ + --INPUT $bam \\ + --OUTPUT ${prefix}.bam \\ + --REFERENCE_SEQUENCE $fasta \\ + --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.bam + touch ${prefix}.bam.bai + touch ${prefix}.MarkDuplicates.metrics.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) + END_VERSIONS + """ +} diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml new file mode 100644 index 00000000..f7693d2f --- /dev/null +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -0,0 +1,71 @@ +name: picard_markduplicates +description: Locate and tag duplicate reads in a BAM file +keywords: + - markduplicates + - pcr + - duplicates + - bam + - sam + - cram +tools: + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://broadinstitute.github.io/picard/ + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam,cram,sam}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference genome fasta index + pattern: "*.{fai}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" + - bai: + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag + pattern: "*.{bai}" + - metrics: + type: file + description: Duplicate metrics file generated by picard + pattern: "*.{metrics.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@projectoriented" + - "@ramprasadn" diff --git a/null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt b/null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt new file mode 100644 index 00000000..6b739acd --- /dev/null +++ b/null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt @@ -0,0 +1 @@ +task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar From 0c3ffaed91d6129217bdd6be8c9fddb002b70e21 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:27:33 +0100 Subject: [PATCH 174/264] correct typo --- subworkflows/local/fusioninspector_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 640b25fd..e616ee5b 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -1,4 +1,4 @@ -include { AGAT_CONVERTSPGFF2TSV } from '../../modules/nf-core/agat/visualisation/main' +include { AGAT_CONVERTSPGFF2TSV } from '../../modules/nf-core/agat/convertspgff2tsv/main' include { ARRIBA_VISUALISATION } from '../../modules/local/arriba/visualisation/main' include { CAT_CAT } from '../../modules/nf-core/cat/cat/main' include { VCF_COLLECT } from '../../modules/local/vcf_collect/main' From ba55fa3fdffda0b8c280e3807702bf4889b239eb Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:08:31 +0100 Subject: [PATCH 175/264] vcf_collect takes tsv_coding_effect channel instead of tsv --- modules/local/fusioninspector/main.nf | 17 +++++++++++------ subworkflows/local/fusioninspector_workflow.nf | 2 +- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf index 1b1a7169..11013837 100644 --- a/modules/local/fusioninspector/main.nf +++ b/modules/local/fusioninspector/main.nf @@ -10,10 +10,11 @@ process FUSIONINSPECTOR { path reference output: - tuple val(meta), path("*FusionInspector.fusions.tsv") , emit: tsv - tuple val(meta), path("*.gtf") , emit: out_gtf - path "*" , emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*FusionInspector.fusions.tsv") , emit: tsv + tuple val(meta), path("*FusionInspector.fusions.tsv.annotated.coding_effect") , emit: tsv_coding_effect + tuple val(meta), path("*.gtf") , emit: out_gtf + path "*" , emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -40,9 +41,13 @@ process FUSIONINSPECTOR { """ stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ - touch FusionInspector.log - touch FusionInspector.fusions.tsv + touch ${prefix}.FusionInspector.log + touch ${prefix}.FusionInspector.fusions.tsv + touch ${prefix}.FusionInspector.fusions.tsv.annotated.coding_effect + touch ${prefix}.gtf cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index e616ee5b..32173e81 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -45,7 +45,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { AGAT_CONVERTSPGFF2TSV(FUSIONINSPECTOR.out.out_gtf) ch_versions = ch_versions.mix(AGAT_CONVERTSPGFF2TSV.out.versions) - fusion_data = FUSIONINSPECTOR.out.tsv.join(AGAT_CONVERTSPGFF2TSV.out.tsv).join(fusionreport_out) + fusion_data = FUSIONINSPECTOR.out.tsv_coding_effect.join(AGAT_CONVERTSPGFF2TSV.out.tsv).join(fusionreport_out) VCF_COLLECT(fusion_data, ch_hgnc_ref, ch_hgnc_date) ch_versions = ch_versions.mix(VCF_COLLECT.out.versions) From 1b9c18115689e32039b56f40dbbd90731f572031 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:36:47 +0100 Subject: [PATCH 176/264] remove empty entry --- bin/vcf_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index ec08e432..cd268ac1 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -286,7 +286,7 @@ def column_manipulation(df): # INFO df.loc[index, "INFO"] = ( "SVTYPE=BND;CHRA={};CHRB={};GENEA={};GENEB={};POSA={};POSB={};ORIENTATION={},{};FOUND_DB={};" - "FOUND_IN={};;TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" + "FOUND_IN={};TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" "TRANSCRIPT_VERSION_A={};TRANSCRIPT_VERSION_B={};HGNC_ID_A={};HGNC_ID_B={};EXON_NUMBER_A={};" "EXON_NUMBER_B={};ANNOTATIONS={}".format( row["ChromosomeA"], From edc1a42d47f36814b1c5cf9af91ba5b46acd5de4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 12:42:42 +0100 Subject: [PATCH 177/264] update arriba --- CHANGELOG.md | 1 + modules/local/arriba/download/main.nf | 20 ++++++++++---------- modules/local/arriba/visualisation/main.nf | 6 +++--- nextflow.config | 8 ++++---- 4 files changed, 18 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a071696..0e74c70b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420) - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) +- `arriba` updated to 2.4.0 ### Fixed diff --git a/modules/local/arriba/download/main.nf b/modules/local/arriba/download/main.nf index 166ed69f..d59c123b 100644 --- a/modules/local/arriba/download/main.nf +++ b/modules/local/arriba/download/main.nf @@ -13,11 +13,11 @@ process ARRIBA_DOWNLOAD { script: """ - wget https://github.com/suhrig/arriba/releases/download/v2.3.0/arriba_v2.3.0.tar.gz -O arriba_v2.3.0.tar.gz - tar -xzvf arriba_v2.3.0.tar.gz - rm arriba_v2.3.0.tar.gz - mv arriba_v2.3.0/database/* . - rm -r arriba_v2.3.0 + wget https://github.com/suhrig/arriba/releases/download/v2.3.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz + tar -xzvf arriba_v2.4.0.tar.gz + rm arriba_v2.4.0.tar.gz + mv arriba_v2.4.0/database/* . + rm -r arriba_v2.4.0 cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -27,11 +27,11 @@ process ARRIBA_DOWNLOAD { stub: """ - touch blacklist_hg38_GRCh38_v2.3.0.tsv.gz - touch protein_domains_hg38_GRCh38_v2.3.0.gff3 - touch cytobands_hg38_GRCh38_v2.3.0.tsv - touch known_fusions_hg38_GRCh38_v2.3.0.tsv.gz - touch protein_domains_hg38_GRCh38_v2.3.0.gff3 + touch blacklist_hg38_GRCh38_v2.4.0.tsv.gz + touch protein_domains_hg38_GRCh38_v2.4.0.gff3 + touch cytobands_hg38_GRCh38_v2.4.0.tsv + touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz + touch protein_domains_hg38_GRCh38_v2.4.0.gff3 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/arriba/visualisation/main.nf b/modules/local/arriba/visualisation/main.nf index 5805a904..cc120119 100644 --- a/modules/local/arriba/visualisation/main.nf +++ b/modules/local/arriba/visualisation/main.nf @@ -2,10 +2,10 @@ process ARRIBA_VISUALISATION { tag "$meta.id" label 'process_medium' - conda "bioconda::arriba=2.3.0" + conda "bioconda::arriba=2.4.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/arriba:2.3.0--haa8aa89_0' : - 'quay.io/biocontainers/arriba:2.3.0--haa8aa89_0' }" + 'https://depot.galaxyproject.org/singularity/arriba:2.4.0--h0033a41_2' : + 'biocontainers/arriba:2.4.0--h0033a41_2' }" input: tuple val(meta), path(bam), path(bai), path(fusions) diff --git a/nextflow.config b/nextflow.config index 925d7a36..5f1e3c2c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -66,10 +66,10 @@ params { // Path to references ensembl_ref = "${params.genomes_base}/ensembl" arriba_ref = "${params.genomes_base}/arriba" - arriba_ref_blacklist = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.3.0.tsv.gz" - arriba_ref_cytobands = "${params.genomes_base}/arriba/cytobands_hg38_GRCh38_v2.3.0.tsv" - arriba_ref_known_fusions = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.3.0.tsv.gz" - arriba_ref_protein_domains = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.3.0.gff3" + arriba_ref_blacklist = "${params.genomes_base}/arriba/blacklist_hg38_GRCh38_v2.4.0.tsv.gz" + arriba_ref_cytobands = "${params.genomes_base}/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv" + arriba_ref_known_fusions = "${params.genomes_base}/arriba/known_fusions_hg38_GRCh38_v2.4.0.tsv.gz" + arriba_ref_protein_domains = "${params.genomes_base}/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3" fusioncatcher_ref = "${params.genomes_base}/fusioncatcher/human_v102" starfusion_ref = "${params.genomes_base}/starfusion/ctat_genome_lib_build_dir" starindex_ref = "${params.genomes_base}/star" From 775444e4fb7dc863b7f008a79632200e73b03498 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 15:15:23 +0100 Subject: [PATCH 178/264] make optional gtf and coding effectsg --- modules/local/fusioninspector/main.nf | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/modules/local/fusioninspector/main.nf b/modules/local/fusioninspector/main.nf index 11013837..c7fcd3f0 100644 --- a/modules/local/fusioninspector/main.nf +++ b/modules/local/fusioninspector/main.nf @@ -10,11 +10,11 @@ process FUSIONINSPECTOR { path reference output: - tuple val(meta), path("*FusionInspector.fusions.tsv") , emit: tsv - tuple val(meta), path("*FusionInspector.fusions.tsv.annotated.coding_effect") , emit: tsv_coding_effect - tuple val(meta), path("*.gtf") , emit: out_gtf - path "*" , emit: output - path "versions.yml" , emit: versions + tuple val(meta), path("*FusionInspector.fusions.tsv") , emit: tsv + tuple val(meta), path("*.coding_effect") , optional:true, emit: tsv_coding_effect + tuple val(meta), path("*.gtf") , optional:true, emit: out_gtf + path "*" , emit: output + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -42,7 +42,6 @@ process FUSIONINSPECTOR { stub: def prefix = task.ext.prefix ?: "${meta.id}" - """ touch ${prefix}.FusionInspector.log touch ${prefix}.FusionInspector.fusions.tsv From 4a38147d79fa7a59032c38c689b54034ad15e106 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 16:36:03 +0100 Subject: [PATCH 179/264] remove HGNC: from HGNC id column --- bin/vcf_collect.py | 1 + modules.json | 5 -- modules/nf-core/picard/markduplicates/main.nf | 65 ----------------- .../nf-core/picard/markduplicates/meta.yml | 71 ------------------- .../execution_trace_2023-11-01_15-05-02.txt | 1 - 5 files changed, 1 insertion(+), 142 deletions(-) delete mode 100644 modules/nf-core/picard/markduplicates/main.nf delete mode 100644 modules/nf-core/picard/markduplicates/meta.yml delete mode 100644 null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index cd268ac1..39da16ba 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -352,6 +352,7 @@ def build_hgnc_dataframe(file): Build a DataFrame from HGNC input file, extracting 'hgnc_id' and 'ensembl_gene_id' columns. """ df = pd.read_csv(file, sep="\t", low_memory=False) + df['hgnc_id'] = df['hgnc_id'].str.replace("HGNC:","") return df[["hgnc_id", "ensembl_gene_id"]].dropna() diff --git a/modules.json b/modules.json index beb0e954..a6ffdfd5 100644 --- a/modules.json +++ b/modules.json @@ -70,11 +70,6 @@ "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", "installed_by": ["modules"] }, - "picard/markduplicates": { - "branch": "master", - "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448", - "installed_by": ["modules"] - }, "samtools/faidx": { "branch": "master", "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf deleted file mode 100644 index ebfa0864..00000000 --- a/modules/nf-core/picard/markduplicates/main.nf +++ /dev/null @@ -1,65 +0,0 @@ -process PICARD_MARKDUPLICATES { - tag "$meta.id" - label 'process_medium' - - conda "bioconda::picard=3.0.0" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" - - input: - tuple val(meta), path(bam) - tuple val(meta2), path(fasta) - tuple val(meta3), path(fai) - - output: - tuple val(meta), path("*.bam") , emit: bam - tuple val(meta), path("*.bai") , optional:true, emit: bai - tuple val(meta), path("*.metrics.txt"), emit: metrics - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def avail_mem = 3072 - if (!task.memory) { - log.info '[Picard MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' - } else { - avail_mem = (task.memory.mega*0.8).intValue() - } - - if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - - """ - picard \\ - -Xmx${avail_mem}M \\ - MarkDuplicates \\ - $args \\ - --INPUT $bam \\ - --OUTPUT ${prefix}.bam \\ - --REFERENCE_SEQUENCE $fasta \\ - --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" - """ - touch ${prefix}.bam - touch ${prefix}.bam.bai - touch ${prefix}.MarkDuplicates.metrics.txt - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:) - END_VERSIONS - """ -} diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml deleted file mode 100644 index f7693d2f..00000000 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ /dev/null @@ -1,71 +0,0 @@ -name: picard_markduplicates -description: Locate and tag duplicate reads in a BAM file -keywords: - - markduplicates - - pcr - - duplicates - - bam - - sam - - cram -tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ["MIT"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference genome fasta index - pattern: "*.{fai}" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" - - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" - - metrics: - type: file - description: Duplicate metrics file generated by picard - pattern: "*.{metrics.txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@projectoriented" - - "@ramprasadn" diff --git a/null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt b/null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt deleted file mode 100644 index 6b739acd..00000000 --- a/null/pipeline_info/execution_trace_2023-11-01_15-05-02.txt +++ /dev/null @@ -1 +0,0 @@ -task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar From 6f2a4ea24d3c6f1004e74fab5c93d898c5ebb1c5 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 17:06:07 +0100 Subject: [PATCH 180/264] fix hgnc date timestamping --- modules/local/hgnc/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/hgnc/main.nf b/modules/local/hgnc/main.nf index 7211cb71..1b3808f6 100644 --- a/modules/local/hgnc/main.nf +++ b/modules/local/hgnc/main.nf @@ -19,7 +19,7 @@ process HGNC_DOWNLOAD { script: """ wget https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt - date+%Y-%m-%d/%H:%M: > HGNC-DB-timestamp.txt + date +%Y-%m-%d/%H:%M > HGNC-DB-timestamp.txt cat <<-END_VERSIONS > versions.yml "${task.process}": From 0b4f60f6789c9ef1b1275aeb5f15f1a79f746644 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 17:09:47 +0100 Subject: [PATCH 181/264] fix typo --- modules/local/arriba/download/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/local/arriba/download/main.nf b/modules/local/arriba/download/main.nf index d59c123b..860439ad 100644 --- a/modules/local/arriba/download/main.nf +++ b/modules/local/arriba/download/main.nf @@ -13,7 +13,7 @@ process ARRIBA_DOWNLOAD { script: """ - wget https://github.com/suhrig/arriba/releases/download/v2.3.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz + wget https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz tar -xzvf arriba_v2.4.0.tar.gz rm arriba_v2.4.0.tar.gz mv arriba_v2.4.0/database/* . From f4c091214c983584bb933ec039a177455ab787c6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 21:43:14 +0100 Subject: [PATCH 182/264] black --- bin/vcf_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 39da16ba..4b3ec199 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -352,7 +352,7 @@ def build_hgnc_dataframe(file): Build a DataFrame from HGNC input file, extracting 'hgnc_id' and 'ensembl_gene_id' columns. """ df = pd.read_csv(file, sep="\t", low_memory=False) - df['hgnc_id'] = df['hgnc_id'].str.replace("HGNC:","") + df["hgnc_id"] = df["hgnc_id"].str.replace("HGNC:", "") return df[["hgnc_id", "ensembl_gene_id"]].dropna() From a641b172522408cae7060e5b2b22ed1b65f773ed Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 6 Nov 2023 21:47:17 +0100 Subject: [PATCH 183/264] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e74c70b..c9dcad59 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420) - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) -- `arriba` updated to 2.4.0 +- `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) ### Fixed From 4337f4ae1653361393190618077291b14d08ca76 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 7 Nov 2023 21:49:47 +0100 Subject: [PATCH 184/264] add support for case fusioninspector filters out a fusion from fusionreport --- bin/vcf_collect.py | 41 ++++++++++++++++++++++++++--------------- 1 file changed, 26 insertions(+), 15 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 4b3ec199..408abfe9 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -11,7 +11,7 @@ logger = logging.getLogger() -def vcf_collect(fusioninspector_in_file, fusionreport_in_file, gtf, hgnc, sample, out): +def vcf_collect(fusioninspector_in_file, fusionreport_in_file, sample, hgnc, gtf, out): """ Process FusionInspector and FusionReport data, merge with GTF from FusionInspector and HGNC database, @@ -33,14 +33,17 @@ def vcf_collect(fusioninspector_in_file, fusionreport_in_file, gtf, hgnc, sample .reset_index() ) - df = build_hgnc_dataframe(hgnc).merge( + df = build_hgcn_dataframe(hgnc).merge( merged_df, how="right", left_on="ensembl_gene_id", right_on="Left_ensembl_gene_id" ) df = df.rename(columns={"hgnc_id": "Left_hgnc_id"}) - df = build_hgnc_dataframe(hgnc).merge(df, how="right", left_on="ensembl_gene_id", right_on="Right_ensembl_gene_id") + df = build_hgcn_dataframe(hgnc).merge(df, how="right", left_on="ensembl_gene_id", right_on="Right_ensembl_gene_id") df = df.rename(columns={"hgnc_id": "Right_hgnc_id"}) gtf_df = build_gtf_dataframe(gtf) all_df = df.merge(gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id") + all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].fillna(0) + all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].astype(int) + all_df = all_df[(all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])] all_df = all_df.rename(columns={"transcript_version": "Left_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Left_exon_number"}) @@ -73,7 +76,10 @@ def vcf_collect(fusioninspector_in_file, fusionreport_in_file, gtf, hgnc, sample ] ].drop_duplicates() all_df = all_df.merge(gtf_df, how="left", left_on="CDS_RIGHT_ID", right_on="Transcript_id") + all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].fillna(0) + all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].astype(int) all_df = all_df[(all_df["PosB"] >= all_df["orig_start"]) & (all_df["PosB"] <= all_df["orig_end"])] + all_df = all_df.rename(columns={"transcript_version": "Right_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Right_exon_number"}) all_df = all_df[ @@ -195,7 +201,6 @@ def build_fusioninspector_dataframe(file): df = df.rename(columns={"#FusionName": "FUSION"}) df[["ChromosomeA", "PosA", "Strand1"]] = df["LeftBreakpoint"].str.split(":", expand=True) df[["ChromosomeB", "PosB", "Strand2"]] = df["RightBreakpoint"].str.split(":", expand=True) - df[["GeneA", "GeneB"]] = df["FUSION"].str.split("--", expand=True) df[["LeftGeneName", "Left_ensembl_gene_id"]] = df["LeftGene"].str.split("^", expand=True) df[["RightGeneName", "Right_ensembl_gene_id"]] = df["RightGene"].str.split("^", expand=True) return df.set_index(["FUSION"]) @@ -234,11 +239,11 @@ def read_build_fusionreport(fusionreport_file): from_html = [line.split('rows": [')[1] for line in f if 'name="fusion_list' in line] expression = from_html[0].split('], "tool')[0] fusion_report = pd.DataFrame.from_dict(ast.literal_eval(expression)) - if "arriba" not in fusion_report.columns: + if not "arriba" in fusion_report.columns: fusion_report["arriba"] = "" - if "fusioncatcher" not in fusion_report.columns: + if not "fusioncatcher" in fusion_report.columns: fusion_report["fusioncatcher"] = "" - if "starfusion" not in fusion_report.columns: + if not "starfusion" in fusion_report.columns: fusion_report["starfusion"] = "" fusion_report["arriba"] = fusion_report[["arriba"]].apply( replace_value_with_column_name, args=("true", "arriba"), axis=1 @@ -254,7 +259,11 @@ def read_build_fusionreport(fusionreport_file): ) fusion_report.columns = fusion_report.columns.str.upper() fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply(lambda x: ", ".join(x)) - return fusion_report[["FUSION", "TOOLS_HITS", "SCORE", "FOUND_DB", "FOUND_IN"]].set_index(["FUSION"]) + fusion_report[["GeneA", "GeneB"]] = fusion_report["FUSION"].str.split("--", expand=True) + + return fusion_report[["FUSION", "GeneA", "GeneB", "TOOLS_HITS", "SCORE", "FOUND_DB", "FOUND_IN"]].set_index( + ["FUSION"] + ) def column_manipulation(df): @@ -270,10 +279,12 @@ def column_manipulation(df): df["REF"] = "N" df["INFO"] = "" df["Sample"] = "" + df["Strand1"] = df["Strand1"].astype(str) for index, row in df.iterrows(): - # ALT - if not row["Strand1"] in ["+", "-"] or not row["Strand2"] in ["+", "-"]: + if row["Strand1"] == "nan": + df.loc[index, "ALT"] = "nan" + elif not row["Strand1"] in ["+", "-"] or not row["Strand2"] in ["+", "-"]: df.loc[index, "ALT"] = "N[{}:{}[".format(df["ChromosomeB"], row["PosB"]) elif row["Strand1"] == "-" and row["Strand2"] == "-": df.loc[index, "ALT"] = "[{}:{}[N".format(row["ChromosomeB"], row["PosB"]) @@ -283,12 +294,12 @@ def column_manipulation(df): df.loc[index, "ALT"] = "N]{}:{}]".format(row["ChromosomeB"], row["PosB"]) else: df.loc[index, "ALT"] = "N[{}:{}[".format(row["ChromosomeB"], row["PosB"]) - # INFO + df.loc[index, "INFO"] = ( "SVTYPE=BND;CHRA={};CHRB={};GENEA={};GENEB={};POSA={};POSB={};ORIENTATION={},{};FOUND_DB={};" - "FOUND_IN={};TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" - "TRANSCRIPT_VERSION_A={};TRANSCRIPT_VERSION_B={};HGNC_ID_A={};HGNC_ID_B={};EXON_NUMBER_A={};" - "EXON_NUMBER_B={};ANNOTATIONS={}".format( + "FOUND_IN={};;TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" + "TRANSCRIPT_VERSION_A={};TRANSCRIPT_VERSION_B={};HGNC_ID_A={};HGNC_ID_B={};EXON_NUMBER_A={},EXON_NUMBER_B={};" + "ANNOTATIONS={}".format( row["ChromosomeA"], row["ChromosomeB"], row["GeneA"], @@ -347,7 +358,7 @@ def write_vcf(df_to_print, header, out_file): f.write(header.rstrip("\r\n") + "\n" + content) -def build_hgnc_dataframe(file): +def build_hgcn_dataframe(file): """ Build a DataFrame from HGNC input file, extracting 'hgnc_id' and 'ensembl_gene_id' columns. """ From a6c995f6c3313c176f269302173beca532344bb9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 7 Nov 2023 22:28:24 +0100 Subject: [PATCH 185/264] update ci --- .github/workflows/ci.yml | 48 +++++++--------------------------------- 1 file changed, 8 insertions(+), 40 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 17f01186..09f52fe5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,6 +26,9 @@ jobs: NXF_VER: - "23.04.0" - "latest-everything" + trim_parameters: + - "--fastp_trim false" + - "--fastp_trim true" steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -35,51 +38,16 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Dry test arriba build + - name: Dry test build run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ - --outdir /home/runner/work/rnafusion/rnafusion/results --arriba \ + --outdir /home/runner/work/rnafusion/rnafusion/results --all \ --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - name: Dry test arriba + - name: Dry test run run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --arriba \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test fusioncatcher build - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub --build_references \ - --outdir /home/runner/work/rnafusion/rnafusion/results --fusioncatcher \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} + --outdir /home/runner/work/rnafusion/rnafusion/results --all matrix.trim_parameters \ + --genomes_base /home/runner/work/rnafusion/rnafusion/results/references - - name: Dry test fusioncatcher - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --fusioncatcher \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test starfusion build - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub build_references \ - --outdir /home/runner/work/rnafusion/rnafusion/results --starfusion \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test starfusion - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --starfusion \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} - - - name: Dry test stingtie - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --stringtie \ - --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \ - --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }} From e8b58d4fbcb481e2913852f696689917d0a736aa Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 7 Nov 2023 22:30:25 +0100 Subject: [PATCH 186/264] prettier --- .github/workflows/ci.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 09f52fe5..33f320ec 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,8 +27,8 @@ jobs: - "23.04.0" - "latest-everything" trim_parameters: - - "--fastp_trim false" - - "--fastp_trim true" + - "--fastp_trim false" + - "--fastp_trim true" steps: - name: Check out pipeline code uses: actions/checkout@v3 @@ -50,4 +50,3 @@ jobs: nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ --outdir /home/runner/work/rnafusion/rnafusion/results --all matrix.trim_parameters \ --genomes_base /home/runner/work/rnafusion/rnafusion/results/references - From 50ab173f0db4ec9549724123ddbea644d8e5d5ab Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 7 Nov 2023 22:36:21 +0100 Subject: [PATCH 187/264] make matrix a parameter not a string --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 33f320ec..6f960cad 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -48,5 +48,5 @@ jobs: - name: Dry test run run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \ - --outdir /home/runner/work/rnafusion/rnafusion/results --all matrix.trim_parameters \ + --outdir /home/runner/work/rnafusion/rnafusion/results --all ${{ matrix.trim_parameters }} \ --genomes_base /home/runner/work/rnafusion/rnafusion/results/references From 7b8cc873ef98b3a14dd16ddd02b90203137c8868 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 7 Nov 2023 22:57:37 +0100 Subject: [PATCH 188/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9dcad59..42489291 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) +- CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430) ### Fixed From fb70a6b194969b7b9dead82334673985fec44107 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 11:58:39 +0100 Subject: [PATCH 189/264] update fusionreport to 2.1.5p6 --- modules/local/fusionreport/detect/main.nf | 2 +- modules/local/fusionreport/download/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index ac03bded..656334c4 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p5" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p6" input: diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index e18955cc..1632b2cf 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -4,7 +4,7 @@ process FUSIONREPORT_DOWNLOAD { // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p5" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p6" input: val(username) From bcd0fa8fb921a6145e612ffa8d263f8c5a6b6021 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 12:01:28 +0100 Subject: [PATCH 190/264] remove unneccessary comments --- modules/local/fusionreport/detect/main.nf | 1 - modules/local/fusionreport/download/main.nf | 1 - 2 files changed, 2 deletions(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 656334c4..8b7b55af 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -2,7 +2,6 @@ process FUSIONREPORT { tag "$meta.id" label 'process_medium' - // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" container "docker.io/clinicalgenomics/fusion-report:2.1.5p6" diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index 1632b2cf..500e11b5 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -2,7 +2,6 @@ process FUSIONREPORT_DOWNLOAD { tag 'fusionreport' label 'process_medium' - // Note: 2.7X indices incompatible with AWS iGenomes. conda "bioconda::star=2.7.9a" container "docker.io/clinicalgenomics/fusion-report:2.1.5p6" From 457bdac8759d97fb3cbea1b65ebe3a5991969432 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 12:03:09 +0100 Subject: [PATCH 191/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9dcad59..46cad4da 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) +- Update `fusion-report` to 2.1.5p6 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) ### Fixed From be99aef3a95573574dc9a9bac357dc20fac66f5d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 13:14:40 +0100 Subject: [PATCH 192/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9dcad59..81535f94 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) +- Change megafusion into vcf_collect, taking into account e.g. the annotation and coding effects outputs from fusioninspector, HGNC ids, frame status... [#414](https://github.com/nf-core/rnafusion/pull/414) ### Fixed From 72ed5b136d2ec30091a556ff3f7a541bbac09c73 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 13:40:20 +0100 Subject: [PATCH 193/264] update awstest --- .github/workflows/awstest.yml | 128 +--------------------------------- .nf-test.log | 2 + 2 files changed, 5 insertions(+), 125 deletions(-) create mode 100644 .nf-test.log diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index d43fe90b..b72a293b 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: # Launch workflow using Tower CLI tool action - - name: Launch build arriba workflow via tower + - name: Launch build references workflow via tower uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -25,7 +25,7 @@ jobs: "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", "cosmic_username": "${{ secrets.cosmic_username }}", "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "arriba": true, + "all": true, "stub": true, "build_references": true } @@ -50,129 +50,7 @@ jobs: "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", "cosmic_username": "${{ secrets.cosmic_username }}", "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "arriba": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch build starfusion workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "starfusion": true, - "build_references": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch starfusion workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "starfusion": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch build fusioncatcher workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "fusioncatcher": true, - "build_references": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch fusioncatcher workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "fusioncatcher": true, - "stub": true - } - profiles: test,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch stringtie workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "stringtie": true, + "all": true, "stub": true } profiles: test,aws_tower diff --git a/.nf-test.log b/.nf-test.log new file mode 100644 index 00000000..d46827bf --- /dev/null +++ b/.nf-test.log @@ -0,0 +1,2 @@ +Nov-08 13:32:43.869 [main] INFO com.askimed.nf.test.App - nf-test 0.8.1 +Nov-08 13:32:43.902 [main] INFO com.askimed.nf.test.App - Arguments: [version] From 867626731b7ef6712934a2c1dfedbe1ba093a090 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 13:46:55 +0100 Subject: [PATCH 194/264] remove nf-test log --- .nf-test.log | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 .nf-test.log diff --git a/.nf-test.log b/.nf-test.log deleted file mode 100644 index d46827bf..00000000 --- a/.nf-test.log +++ /dev/null @@ -1,2 +0,0 @@ -Nov-08 13:32:43.869 [main] INFO com.askimed.nf.test.App - nf-test 0.8.1 -Nov-08 13:32:43.902 [main] INFO com.askimed.nf.test.App - Arguments: [version] From 262546d20f2c470dd78f85d803548591a3bd872d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 13:55:33 +0100 Subject: [PATCH 195/264] update awsfulltest --- .github/workflows/awsfulltest.yml | 131 +----------------------------- 1 file changed, 4 insertions(+), 127 deletions(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index f25848e7..d2c448d7 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -13,7 +13,7 @@ jobs: if: github.repository == 'nf-core/rnafusion' runs-on: ubuntu-latest steps: - - name: Launch build arriba workflow via tower + - name: Launch build references workflow via tower uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -28,7 +28,7 @@ jobs: "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", "cosmic_username": "${{ secrets.cosmic_username }}", "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "arriba": true, + "all": true, "build_references": true } profiles: test_full,aws_tower @@ -39,7 +39,7 @@ jobs: tower_action_*.log tower_action_*.json - - name: Launch arriba workflow via tower + - name: Launch run workflow via tower uses: seqeralabs/action-tower-launch@v2 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} @@ -52,129 +52,6 @@ jobs: "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", "cosmic_username": "${{ secrets.cosmic_username }}", "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "arriba": true, + "all": true, } profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch build starfusion workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "starfusion": true, - "build_references": true - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch starfusion workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "starfusion": true, - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch build fusioncatcher workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "fusioncatcher": true, - "build_references": true - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch fusioncatcher workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "fusioncatcher": true, - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json - - - name: Launch stringtie workflow via tower - uses: seqeralabs/action-tower-launch@v2 - with: - workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} - access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} - compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/rnafusion/work-${{ github.sha }} - parameters: | - { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}", - "genomes_base": "s3://${{ secrets.AWS_S3_BUCKET }}/rnafusion/results-${{ github.sha }}/references", - "cosmic_username": "${{ secrets.cosmic_username }}", - "cosmic_passwd": "${{ secrets.cosmic_passwd }}", - "stringtie": true, - } - profiles: test_full,aws_tower - - uses: actions/upload-artifact@v3 - with: - name: Tower debug log file - path: | - tower_action_*.log - tower_action_*.json From c472f63c23c3dd033ca7d5b6fea315b2f5fcaaf4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:10:46 +0100 Subject: [PATCH 196/264] update fusionreport --- CHANGELOG.md | 2 +- modules/local/fusionreport/detect/main.nf | 2 +- modules/local/fusionreport/download/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 46cad4da..058b8459 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) -- Update `fusion-report` to 2.1.5p6 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) +- Update `fusion-report` to 2.1.5p7 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) and rapidjson []() ### Fixed diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 8b7b55af..447bf528 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p6" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p7" input: diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index 500e11b5..9d529426 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT_DOWNLOAD { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p6" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p7" input: val(username) From 65be55e441b7bd17f4f2206a8a05db1bb33f8ea1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 8 Nov 2023 15:11:41 +0100 Subject: [PATCH 197/264] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 058b8459..f23716b1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) -- Update `fusion-report` to 2.1.5p7 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) and rapidjson []() +- Update `fusion-report` to 2.1.5p7 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) and rapidjson [#434](https://github.com/nf-core/rnafusion/pull/434) ### Fixed From 0a9eacfcc0562d41c8b86cac0d583e12a9b14964 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Thu, 9 Nov 2023 12:28:22 +0100 Subject: [PATCH 198/264] update container for fusionreport --- modules/local/fusionreport/detect/main.nf | 2 +- modules/local/fusionreport/download/main.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 447bf528..6060e0ae 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p7" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p8" input: diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index 9d529426..220b51c9 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT_DOWNLOAD { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p7" + container "docker.io/clinicalgenomics/fusion-report:2.1.5p8" input: val(username) From 7118cd04d59b6478a5972b6006c960d3193aa3c4 Mon Sep 17 00:00:00 2001 From: Eva Caceres Date: Thu, 9 Nov 2023 12:31:47 +0100 Subject: [PATCH 199/264] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f23716b1..b28d1a22 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,7 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) -- Update `fusion-report` to 2.1.5p7 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) and rapidjson [#434](https://github.com/nf-core/rnafusion/pull/434) +- Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432), rapidjson [#434](https://github.com/nf-core/rnafusion/pull/434) and logs [#435](https://github.com/nf-core/rnafusion/pull/435) ### Fixed From 1c109ffcdfb765f49df852636e9bde4b331246e9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 10 Nov 2023 10:34:00 +0100 Subject: [PATCH 200/264] Update bin/vcf_collect.py Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- bin/vcf_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 408abfe9..69d39f34 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -193,7 +193,7 @@ def header_def(sample): ) -def build_fusioninspector_dataframe(file): +def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: """ Read FusionInspector output from a CSV file, preprocess the data, and set 'FUSION' as the index. """ From ff51b1cee25120fc583c9b20ebba37620ac91359 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 10 Nov 2023 10:36:44 +0100 Subject: [PATCH 201/264] Apply suggestions from code review Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- bin/vcf_collect.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 69d39f34..7d43a98a 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -11,7 +11,7 @@ logger = logging.getLogger() -def vcf_collect(fusioninspector_in_file, fusionreport_in_file, sample, hgnc, gtf, out): +def vcf_collect(fusioninspector_in_file: str, fusionreport_in_file: str, sample: str, hgnc: str, gtf: str, out_file) -> None: """ Process FusionInspector and FusionReport data, merge with GTF from FusionInspector and HGNC database, @@ -206,7 +206,7 @@ def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: return df.set_index(["FUSION"]) -def replace_value_with_column_name(row, value_to_replace, column_name): +def replace_value_with_column_name(row: pd.Series, value_to_replace: str, column_name: str) -> str: """ Replace a specific value in a row with the corresponding column name. """ @@ -220,7 +220,7 @@ def replace_value_with_column_name(row, value_to_replace, column_name): return new_values -def concatenate_columns(row): +def concatenate_columns(row: pd.Series) -> str: """ Concatenate non-empty values in a row into a single string separated by commas. """ @@ -228,7 +228,7 @@ def concatenate_columns(row): return ",".join(non_empty_values) -def read_build_fusionreport(fusionreport_file): +def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: """ Read and preprocess fusion-report data from a file, including handling missing tool columns, getting the columns with each tool and create a new FOUND_IN column with all the tool hits. @@ -266,7 +266,7 @@ def read_build_fusionreport(fusionreport_file): ) -def column_manipulation(df): +def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: """ Manipulate and prepare DataFrame for VCF file creation. """ @@ -297,7 +297,7 @@ def column_manipulation(df): df.loc[index, "INFO"] = ( "SVTYPE=BND;CHRA={};CHRB={};GENEA={};GENEB={};POSA={};POSB={};ORIENTATION={},{};FOUND_DB={};" - "FOUND_IN={};;TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" + "FOUND_IN={};TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" "TRANSCRIPT_VERSION_A={};TRANSCRIPT_VERSION_B={};HGNC_ID_A={};HGNC_ID_B={};EXON_NUMBER_A={},EXON_NUMBER_B={};" "ANNOTATIONS={}".format( row["ChromosomeA"], @@ -328,7 +328,7 @@ def column_manipulation(df): return df -def write_vcf(df_to_print, header, out_file): +def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: """ Write a VCF file with a specified DataFrame, header, and output file path. """ @@ -358,7 +358,7 @@ def write_vcf(df_to_print, header, out_file): f.write(header.rstrip("\r\n") + "\n" + content) -def build_hgcn_dataframe(file): +def build_hgcn_dataframe(file: str) -> pd.DataFrame: """ Build a DataFrame from HGNC input file, extracting 'hgnc_id' and 'ensembl_gene_id' columns. """ @@ -367,7 +367,7 @@ def build_hgcn_dataframe(file): return df[["hgnc_id", "ensembl_gene_id"]].dropna() -def build_gtf_dataframe(file): +def build_gtf_dataframe(file: str) -> pd.DataFrame: """ Build a DataFrame from GTF file converted in TSV, extracting relevant columns. """ From de3a105937a8d54ac75dc893ac56b70288156c57 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 09:32:20 +0100 Subject: [PATCH 202/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f87f5165..f4382e81 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) - CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430) +- AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433) - Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) ### Fixed From 92a3dadf2b80eb151746c5217b37d6d44328d953 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 10:04:16 +0100 Subject: [PATCH 203/264] use fstrings --- bin/vcf_collect.py | 47 ++++++++++++++-------------------------------- 1 file changed, 14 insertions(+), 33 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 7d43a98a..c5157512 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -285,46 +285,27 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: if row["Strand1"] == "nan": df.loc[index, "ALT"] = "nan" elif not row["Strand1"] in ["+", "-"] or not row["Strand2"] in ["+", "-"]: - df.loc[index, "ALT"] = "N[{}:{}[".format(df["ChromosomeB"], row["PosB"]) + df.loc[index, "ALT"] = f'N[{df["ChromosomeB"]}:{row["PosB"]}[' elif row["Strand1"] == "-" and row["Strand2"] == "-": - df.loc[index, "ALT"] = "[{}:{}[N".format(row["ChromosomeB"], row["PosB"]) + df.loc[index, "ALT"] = f'[{row["ChromosomeB"]}:{row["PosB"]}[N' elif row["Strand1"] == "+" and row["Strand2"] == "-": - df.loc[index, "ALT"] = "N]{}:{}]".format(row["ChromosomeB"], row["PosB"]) + df.loc[index, "ALT"] = f'N]{row["ChromosomeB"]}:{row["PosB"]}]' elif row["Strand1"] == "-" and row["Strand2"] == "+": - df.loc[index, "ALT"] = "N]{}:{}]".format(row["ChromosomeB"], row["PosB"]) + df.loc[index, "ALT"] = f'N]{row["ChromosomeB"]}:{row["PosB"]}]' else: - df.loc[index, "ALT"] = "N[{}:{}[".format(row["ChromosomeB"], row["PosB"]) + df.loc[index, "ALT"] = f'N[{row["ChromosomeB"]}:{row["PosB"]}[' df.loc[index, "INFO"] = ( - "SVTYPE=BND;CHRA={};CHRB={};GENEA={};GENEB={};POSA={};POSB={};ORIENTATION={},{};FOUND_DB={};" - "FOUND_IN={};TOOL_HITS={};SCORE={};FRAME_STATUS={};TRANSCRIPT_ID_A={};TRANSCRIPT_ID_B={};" - "TRANSCRIPT_VERSION_A={};TRANSCRIPT_VERSION_B={};HGNC_ID_A={};HGNC_ID_B={};EXON_NUMBER_A={},EXON_NUMBER_B={};" - "ANNOTATIONS={}".format( - row["ChromosomeA"], - row["ChromosomeB"], - row["GeneA"], - row["GeneB"], - row["PosA"], - row["PosB"], - row["Strand1"], - row["Strand2"], - row["FOUND_DB"], - row["FOUND_IN"], - row["TOOLS_HITS"], - row["SCORE"], - row["PROT_FUSION_TYPE"], - row["CDS_LEFT_ID"], - row["CDS_RIGHT_ID"], - row["Left_transcript_version"], - row["Right_transcript_version"], - row["Left_hgnc_id"], - row["Right_hgnc_id"], - row["Left_exon_number"], - row["Right_exon_number"], - row["annots"], - ) + f"SVTYPE=BND;CHRA={row['ChromosomeA']};CHRB={row['ChromosomeB']};GENEA={row['GeneA']};GENEB={row['GeneB']};" + f"POSA={row['PosA']};POSB={row['PosB']};ORIENTATION={row['Strand1']},{row['Strand2']};FOUND_DB={row['FOUND_DB']};" + f"FOUND_IN={row['FOUND_IN']};TOOL_HITS={row['TOOLS_HITS']};SCORE={row['SCORE']};FRAME_STATUS={row['PROT_FUSION_TYPE']};" + f"TRANSCRIPT_ID_A={row['CDS_LEFT_ID']};TRANSCRIPT_ID_B={row['CDS_RIGHT_ID']};" + f"TRANSCRIPT_VERSION_A={row['Left_transcript_version']};TRANSCRIPT_VERSION_B={row['Right_transcript_version']};" + f"HGNC_ID_A={row['Left_hgnc_id']};HGNC_ID_B={row['Right_hgnc_id']};" + f"EXON_NUMBER_A={row['Left_exon_number']},EXON_NUMBER_B={row['Right_exon_number']};" + f"ANNOTATIONS={row['annots']}" ) - df.loc[index, "Sample"] = "./1:{}:{}:{}".format(row["JunctionReadCount"], row["SpanningFragCount"], row["FFPM"]) + df.loc[index, "Sample"] = f"./1:{row['JunctionReadCount']}:{row['SpanningFragCount']}:{row['FFPM']}" return df From 7a700f0ff6b00a82e057d32a81ea06f717a7a437 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 10:05:30 +0100 Subject: [PATCH 204/264] add info on GTF output file from fusioninspector --- bin/vcf_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index c5157512..3761a11c 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -22,7 +22,7 @@ def vcf_collect(fusioninspector_in_file: str, fusionreport_in_file: str, sample: fusionreport_in_file (str): Path to FusionReport input file. sample (str): Sample name for the header. hgnc (str): Path to HGNC file. - gtf (str): Path to GTF file. + gtf (str): Path to output GTF file from FusionInspector. out (str): Output VCF file path. Adapted from: https://github.com/J35P312/MegaFusion From 22e4502c76aa635aa142006fd9c926e7ae373d6f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 10:06:59 +0100 Subject: [PATCH 205/264] black --- bin/vcf_collect.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 3761a11c..14855fd6 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -11,7 +11,9 @@ logger = logging.getLogger() -def vcf_collect(fusioninspector_in_file: str, fusionreport_in_file: str, sample: str, hgnc: str, gtf: str, out_file) -> None: +def vcf_collect( + fusioninspector_in_file: str, fusionreport_in_file: str, sample: str, hgnc: str, gtf: str, out_file +) -> None: """ Process FusionInspector and FusionReport data, merge with GTF from FusionInspector and HGNC database, From 1478c1cc226afadb0d826be725d2ef3ddc092090 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 15:12:49 +0100 Subject: [PATCH 206/264] make clearer that fusionreport used is a fork --- docs/output.md | 2 ++ docs/usage.md | 4 ++++ modules/local/fusionreport/detect/meta.yml | 2 +- 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/output.md b/docs/output.md index 92923a53..584ed5b6 100644 --- a/docs/output.md +++ b/docs/output.md @@ -200,6 +200,8 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m ### Fusion-report +Please note that fusion-report is executed from fork https://github.com/Clinical-Genomics/fusion-report +

    Output files diff --git a/docs/usage.md b/docs/usage.md index 32ed1ff6..90725471 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -94,6 +94,10 @@ process { The four `fusion-report` files: `cosmic.db`, `fusiongdb.db`, `fusiongdb2.db`, `mitelman.db` should then be copied into the HPC `/references/fusion_report_db`. +#### Note about fusioncatcher references + +The references are only built based on ensembl version 102. It is not possible currently to use any other version/source. + ## Running the pipeline ### Samplesheet input diff --git a/modules/local/fusionreport/detect/meta.yml b/modules/local/fusionreport/detect/meta.yml index 83ba76c7..ae3601dc 100644 --- a/modules/local/fusionreport/detect/meta.yml +++ b/modules/local/fusionreport/detect/meta.yml @@ -5,7 +5,7 @@ keywords: tools: - fusionreport: description: Tool for parsing outputs from fusion detection tools - homepage: https://github.com/matq007/fusion-report + homepage: https://github.com/Clinical-Genomics/fusion-report documentation: https://matq007.github.io/fusion-report/#/ doi: "10.1101/011650" licence: ["GPL v3"] From e59823c3f7b054e262df0d5bfdd4f693017aba1d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:18:55 +0100 Subject: [PATCH 207/264] fix header typer --- bin/vcf_collect.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 14855fd6..7156a806 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -6,7 +6,8 @@ from pathlib import Path import pandas as pd import ast -from gtfparse import read_gtf +import numpy as np +import csv logger = logging.getLogger() @@ -176,16 +177,16 @@ def header_def(sample): ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ -##INFO=\n\ -##INFO=\n\ -##INFO=\n\ +##INFO=\n\ +##INFO=\n\ +##INFO=\n\ ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ ##INFO=\n\ -##INFO=\n\ +##INFO=\n\ ##FORMAT=\n\ ##FORMAT=\n\ ##FORMAT=\n\ @@ -194,7 +195,6 @@ def header_def(sample): sample ) - def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: """ Read FusionInspector output from a CSV file, preprocess the data, and set 'FUSION' as the index. From afda8fda8c5cb7674b6f437e384ab1537552237a Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:19:02 +0100 Subject: [PATCH 208/264] mend --- conf/modules.config | 1 - modules/local/vcf_collect/main.nf | 8 +++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index f49dd02c..39135aa3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -344,6 +344,5 @@ process { withName: VCF_COLLECT { ext.when = {!params.fusioninspector_only} - ext.prefix = { "${meta.id}_fusion_data" } } } diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index df999204..c634a6a3 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -2,8 +2,10 @@ process VCF_COLLECT { tag "$meta.id" label 'process_single' - conda "bioconda::gtfparse=2.0.1" - container "quay.io/biocontainers/gtfparse:2.0.1--pyh7cba7a3_1" + conda "conda-forge::python=3.8.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'quay.io/biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report) @@ -20,7 +22,7 @@ process VCF_COLLECT { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}.vcf + vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From f14bd90558e09d6dcfaf6190199be5b640247789 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:22:08 +0100 Subject: [PATCH 209/264] Revert "mend" This reverts commit afda8fda8c5cb7674b6f437e384ab1537552237a. --- conf/modules.config | 1 + modules/local/vcf_collect/main.nf | 8 +++----- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 39135aa3..f49dd02c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -344,5 +344,6 @@ process { withName: VCF_COLLECT { ext.when = {!params.fusioninspector_only} + ext.prefix = { "${meta.id}_fusion_data" } } } diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index c634a6a3..df999204 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -2,10 +2,8 @@ process VCF_COLLECT { tag "$meta.id" label 'process_single' - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'quay.io/biocontainers/pandas:1.5.2' }" + conda "bioconda::gtfparse=2.0.1" + container "quay.io/biocontainers/gtfparse:2.0.1--pyh7cba7a3_1" input: tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report) @@ -22,7 +20,7 @@ process VCF_COLLECT { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf + vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From 55d95d1f8c81e78bdabf7e2dfded65b95bd69b67 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:24:02 +0100 Subject: [PATCH 210/264] revert to plain pandas container --- modules/local/vcf_collect/main.nf | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index df999204..c634a6a3 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -2,8 +2,10 @@ process VCF_COLLECT { tag "$meta.id" label 'process_single' - conda "bioconda::gtfparse=2.0.1" - container "quay.io/biocontainers/gtfparse:2.0.1--pyh7cba7a3_1" + conda "conda-forge::python=3.8.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'quay.io/biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report) @@ -20,7 +22,7 @@ process VCF_COLLECT { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}.vcf + vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From 6bc7351dd1bf9e43e5c9c69312594d245841c0dd Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:24:52 +0100 Subject: [PATCH 211/264] sample should just be meta.id, add fusion_data in module for output name --- conf/modules.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index f49dd02c..39135aa3 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -344,6 +344,5 @@ process { withName: VCF_COLLECT { ext.when = {!params.fusioninspector_only} - ext.prefix = { "${meta.id}_fusion_data" } } } From d559232b5da7a028c15b53a80e462ef352ee6dab Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:53:27 +0100 Subject: [PATCH 212/264] remove quotes and flatten the pseudo list in annots --- bin/vcf_collect.py | 22 +++++++++++++++------- 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 7156a806..d52031ef 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -159,7 +159,7 @@ def parse_args(argv=None): return parser.parse_args(argv) -def header_def(sample): +def header_def(sample: str) -> str: """ Define the header of the VCF file """ @@ -195,6 +195,14 @@ def header_def(sample): sample ) + +def convert_to_list(annots_str: str) -> list: + try: + return ast.literal_eval(annots_str) + except (SyntaxError, ValueError): + return np.nan + + def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: """ Read FusionInspector output from a CSV file, preprocess the data, and set 'FUSION' as the index. @@ -205,6 +213,11 @@ def build_fusioninspector_dataframe(file: str) -> pd.DataFrame: df[["ChromosomeB", "PosB", "Strand2"]] = df["RightBreakpoint"].str.split(":", expand=True) df[["LeftGeneName", "Left_ensembl_gene_id"]] = df["LeftGene"].str.split("^", expand=True) df[["RightGeneName", "Right_ensembl_gene_id"]] = df["RightGene"].str.split("^", expand=True) + df["annots"] = ( + df["annots"] + .apply(convert_to_list) + .apply(lambda x: ",".join(map(str, x)) if isinstance(x, list) else str(x) if pd.notna(x) else "") + ) return df.set_index(["FUSION"]) @@ -328,12 +341,7 @@ def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: "FORMAT", "Sample", ] - ].to_csv( - path_or_buf=out_file, - sep="\t", - header=None, - index=False, - ) + ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE) with open(out_file, "r+") as f: content = f.read() From d0a4bf2202945fcef640d335d0dddc91a00e7408 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:53:50 +0100 Subject: [PATCH 213/264] back to original container --- modules/local/vcf_collect/main.nf | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index c634a6a3..5028b2c5 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -2,10 +2,8 @@ process VCF_COLLECT { tag "$meta.id" label 'process_single' - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : - 'quay.io/biocontainers/pandas:1.5.2' }" + conda "bioconda::gtfparse=2.0.1" + container "quay.io/biocontainers/gtfparse:2.0.1--pyh7cba7a3_1" input: tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report) From b46894252fc26553a02a1bad13162a6b6113e595 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 13 Nov 2023 20:12:36 +0100 Subject: [PATCH 214/264] revert to pandas --- modules/local/vcf_collect/main.nf | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index 5028b2c5..c634a6a3 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -2,8 +2,10 @@ process VCF_COLLECT { tag "$meta.id" label 'process_single' - conda "bioconda::gtfparse=2.0.1" - container "quay.io/biocontainers/gtfparse:2.0.1--pyh7cba7a3_1" + conda "conda-forge::python=3.8.3" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : + 'quay.io/biocontainers/pandas:1.5.2' }" input: tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report) From 960db4cf090ced0022d7956dcfcf70ec3f7ded1c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Tue, 14 Nov 2023 22:52:38 +0100 Subject: [PATCH 215/264] apply fixes --- bin/vcf_collect.py | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index d52031ef..8e15ccfc 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -11,9 +11,11 @@ logger = logging.getLogger() +# vcf_collect(args.fusioninspector, args.fusionreport, args.fusioninspector_gtf, args.hgnc, args.sample, args.out) + def vcf_collect( - fusioninspector_in_file: str, fusionreport_in_file: str, sample: str, hgnc: str, gtf: str, out_file + fusioninspector_in_file: str, fusionreport_in_file: str, gtf: str, hgnc: str, sample: str, out_file ) -> None: """ Process FusionInspector and FusionReport data, @@ -25,7 +27,7 @@ def vcf_collect( fusionreport_in_file (str): Path to FusionReport input file. sample (str): Sample name for the header. hgnc (str): Path to HGNC file. - gtf (str): Path to output GTF file from FusionInspector. + gtf (str): Path to output GTF file from FusionInspector in TSV format. out (str): Output VCF file path. Adapted from: https://github.com/J35P312/MegaFusion @@ -116,7 +118,7 @@ def vcf_collect( ] ].drop_duplicates() - return write_vcf(column_manipulation(all_df), header_def(sample), out) + return write_vcf(column_manipulation(all_df), header_def(sample), out_file) def parse_args(argv=None): @@ -371,7 +373,12 @@ def build_gtf_dataframe(file: str) -> pd.DataFrame: def main(argv=None): """Coordinate argument parsing and program execution.""" args = parse_args(argv) - if not args.fusioninspector.is_file() or not args.fusionreport.is_file(): + if ( + not args.fusioninspector.is_file() + or not args.fusionreport.is_file() + or not args.fusioninspector_gtf + or not args.hgnc + ): logger.error(f"The given input file {args.fusioninspector} or {args.fusionreport} was not found!") sys.exit(2) vcf_collect(args.fusioninspector, args.fusionreport, args.fusioninspector_gtf, args.hgnc, args.sample, args.out) From 852c6ac8290aa3819f51ee0e4ebcd36b465caade Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 15 Nov 2023 09:33:18 +0100 Subject: [PATCH 216/264] compress vcf output --- bin/vcf_collect.py | 5 +++-- modules/local/vcf_collect/main.nf | 4 ++-- modules/local/vcf_collect/meta.yml | 4 ++-- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 8e15ccfc..6a97fb50 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -8,6 +8,7 @@ import ast import numpy as np import csv +import gzip logger = logging.getLogger() @@ -343,9 +344,9 @@ def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: "FORMAT", "Sample", ] - ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE) + ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE, compression='gzip') - with open(out_file, "r+") as f: + with gzip.open(out_file, "r+") as f: content = f.read() f.seek(0, 0) f.write(header.rstrip("\r\n") + "\n" + content) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index c634a6a3..42f94c40 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -14,7 +14,7 @@ process VCF_COLLECT { output: path "versions.yml" , emit: versions - tuple val(meta), path("*vcf") , emit: vcf + tuple val(meta), path("*vcf.gz") , emit: vcf when: task.ext.when == null || task.ext.when @@ -22,7 +22,7 @@ process VCF_COLLECT { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf + vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/vcf_collect/meta.yml b/modules/local/vcf_collect/meta.yml index 40bdd6c0..de4667bb 100644 --- a/modules/local/vcf_collect/meta.yml +++ b/modules/local/vcf_collect/meta.yml @@ -32,8 +32,8 @@ output: pattern: "versions.yml" - vcf: type: file - description: File containing the summary of all fusions as vcf file - pattern: "*.tsv" + description: File containing the summary of all fusions as compressed vcf file + pattern: "*.vcf.gz" authors: - "@rannick" From 9643ed80b047441eda5735a6c61857a6e5b0a12c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 15 Nov 2023 09:33:40 +0100 Subject: [PATCH 217/264] black --- bin/vcf_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 6a97fb50..4d677de0 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -344,7 +344,7 @@ def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: "FORMAT", "Sample", ] - ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE, compression='gzip') + ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE, compression="gzip") with gzip.open(out_file, "r+") as f: content = f.read() From bb703dd103fa91ab4e2f28b12c673d21dbbe6232 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 15 Nov 2023 09:44:42 +0100 Subject: [PATCH 218/264] modules updatge --- modules.json | 40 +- .../agat/convertspgff2tsv/environment.yml | 1 + modules/nf-core/cat/cat/environment.yml | 7 + modules/nf-core/cat/cat/main.nf | 2 +- modules/nf-core/cat/cat/meta.yml | 7 +- modules/nf-core/cat/cat/tests/main.nf.test | 153 ++++++ .../nf-core/cat/cat/tests/main.nf.test.snap | 121 +++++ .../cat/tests/nextflow_unzipped_zipped.config | 6 + .../cat/tests/nextflow_zipped_unzipped.config | 8 + modules/nf-core/cat/cat/tests/tags.yml | 2 + modules/nf-core/cat/fastq/environment.yml | 7 + modules/nf-core/cat/fastq/main.nf | 2 +- modules/nf-core/cat/fastq/meta.yml | 4 +- modules/nf-core/cat/fastq/tests/main.nf.test | 143 ++++++ .../nf-core/cat/fastq/tests/main.nf.test.snap | 78 +++ modules/nf-core/cat/fastq/tests/tags.yml | 2 + .../dumpsoftwareversions/environment.yml | 7 + .../custom/dumpsoftwareversions/main.nf | 6 +- .../custom/dumpsoftwareversions/meta.yml | 7 +- .../dumpsoftwareversions/tests/main.nf.test | 38 ++ .../tests/main.nf.test.snap | 27 + .../dumpsoftwareversions/tests/tags.yml | 2 + modules/nf-core/fastp/environment.yml | 7 + modules/nf-core/fastp/main.nf | 2 +- modules/nf-core/fastp/meta.yml | 4 +- modules/nf-core/fastp/tests/main.nf.test | 485 ++++++++++++++++++ modules/nf-core/fastp/tests/main.nf.test.snap | 52 ++ modules/nf-core/fastp/tests/nextflow.config | 6 + modules/nf-core/fastp/tests/tags.yml | 2 + modules/nf-core/fastqc/environment.yml | 7 + modules/nf-core/fastqc/main.nf | 6 +- modules/nf-core/fastqc/meta.yml | 5 + modules/nf-core/fastqc/tests/main.nf.test | 23 +- .../nf-core/fastqc/tests/main.nf.test.snap | 10 + modules/nf-core/fastqc/tests/tags.yml | 2 + .../gatk4/bedtointervallist/environment.yml | 7 + .../nf-core/gatk4/bedtointervallist/main.nf | 2 +- .../nf-core/gatk4/bedtointervallist/meta.yml | 3 + .../createsequencedictionary/environment.yml | 7 + .../gatk4/createsequencedictionary/main.nf | 2 +- .../gatk4/createsequencedictionary/meta.yml | 4 +- .../gatk4/markduplicates/environment.yml | 8 + modules/nf-core/gatk4/markduplicates/main.nf | 2 +- modules/nf-core/gatk4/markduplicates/meta.yml | 12 +- modules/nf-core/multiqc/environment.yml | 7 + modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/meta.yml | 11 +- .../collectinsertsizemetrics/environment.yml | 7 + .../picard/collectinsertsizemetrics/main.nf | 6 +- .../picard/collectinsertsizemetrics/meta.yml | 5 +- .../picard/collectwgsmetrics/environment.yml | 8 + .../nf-core/picard/collectwgsmetrics/main.nf | 6 +- .../nf-core/picard/collectwgsmetrics/meta.yml | 5 + .../nf-core/samtools/faidx/environment.yml | 7 + modules/nf-core/samtools/faidx/main.nf | 2 +- modules/nf-core/samtools/faidx/meta.yml | 4 + .../nf-core/samtools/index/environment.yml | 7 + modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/index/meta.yml | 4 + modules/nf-core/samtools/sort/environment.yml | 7 + modules/nf-core/samtools/sort/main.nf | 2 +- modules/nf-core/samtools/sort/meta.yml | 3 + .../nf-core/samtools/sort/tests/main.nf.test | 70 +++ .../samtools/sort/tests/main.nf.test.snap | 39 ++ .../samtools/sort/tests/nextflow.config | 7 + modules/nf-core/samtools/sort/tests/tags.yml | 3 + modules/nf-core/samtools/view/environment.yml | 7 + modules/nf-core/samtools/view/main.nf | 2 +- modules/nf-core/samtools/view/meta.yml | 5 + modules/nf-core/star/align/environment.yml | 9 + modules/nf-core/star/align/main.nf | 2 +- modules/nf-core/star/align/meta.yml | 6 +- .../star/genomegenerate/environment.yml | 9 + modules/nf-core/star/genomegenerate/main.nf | 2 +- modules/nf-core/star/genomegenerate/meta.yml | 5 +- .../nf-core/stringtie/merge/environment.yml | 7 + modules/nf-core/stringtie/merge/main.nf | 2 +- modules/nf-core/stringtie/merge/meta.yml | 3 +- .../stringtie/stringtie/environment.yml | 7 + modules/nf-core/stringtie/stringtie/main.nf | 2 +- modules/nf-core/stringtie/stringtie/meta.yml | 3 +- 81 files changed, 1531 insertions(+), 86 deletions(-) create mode 100644 modules/nf-core/cat/cat/environment.yml create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config create mode 100644 modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config create mode 100644 modules/nf-core/cat/cat/tests/tags.yml create mode 100644 modules/nf-core/cat/fastq/environment.yml create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/fastq/tests/tags.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml create mode 100644 modules/nf-core/fastp/environment.yml create mode 100644 modules/nf-core/fastp/tests/main.nf.test create mode 100644 modules/nf-core/fastp/tests/main.nf.test.snap create mode 100644 modules/nf-core/fastp/tests/nextflow.config create mode 100644 modules/nf-core/fastp/tests/tags.yml create mode 100644 modules/nf-core/fastqc/environment.yml create mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap create mode 100644 modules/nf-core/fastqc/tests/tags.yml create mode 100644 modules/nf-core/gatk4/bedtointervallist/environment.yml create mode 100644 modules/nf-core/gatk4/createsequencedictionary/environment.yml create mode 100644 modules/nf-core/gatk4/markduplicates/environment.yml create mode 100644 modules/nf-core/multiqc/environment.yml create mode 100644 modules/nf-core/picard/collectinsertsizemetrics/environment.yml create mode 100644 modules/nf-core/picard/collectwgsmetrics/environment.yml create mode 100644 modules/nf-core/samtools/faidx/environment.yml create mode 100644 modules/nf-core/samtools/index/environment.yml create mode 100644 modules/nf-core/samtools/sort/environment.yml create mode 100644 modules/nf-core/samtools/sort/tests/main.nf.test create mode 100644 modules/nf-core/samtools/sort/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/sort/tests/nextflow.config create mode 100644 modules/nf-core/samtools/sort/tests/tags.yml create mode 100644 modules/nf-core/samtools/view/environment.yml create mode 100644 modules/nf-core/star/align/environment.yml create mode 100644 modules/nf-core/star/genomegenerate/environment.yml create mode 100644 modules/nf-core/stringtie/merge/environment.yml create mode 100644 modules/nf-core/stringtie/stringtie/environment.yml diff --git a/modules.json b/modules.json index a6ffdfd5..724634dc 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "agat/convertspgff2tsv": { "branch": "master", - "git_sha": "53e6fd5d80141e00a3b70762f4361f6af1f4303b", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "arriba": { @@ -17,97 +17,97 @@ }, "cat/cat": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", - "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", + "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "fastqc": { "branch": "master", - "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/bedtointervallist": { "branch": "master", - "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "cf8f9ace77aac01caa5c7cb92af5bbda7adb77bd", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/markduplicates": { "branch": "master", - "git_sha": "2aa9c2981930687792ed861b0a5f9ff7bb568a7d", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", + "git_sha": "214d575774c172062924ad3564b4f66655600730", "installed_by": ["modules"] }, "picard/collectinsertsizemetrics": { "branch": "master", - "git_sha": "240937a2a9c30298110753292be041188891f2cb", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "picard/collectwgsmetrics": { "branch": "master", - "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", - "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "samtools/view": { "branch": "master", - "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "star/align": { "branch": "master", - "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "cc08a888069f67cab8120259bddab8032d4c0fe3", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "stringtie/merge": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] } } diff --git a/modules/nf-core/agat/convertspgff2tsv/environment.yml b/modules/nf-core/agat/convertspgff2tsv/environment.yml index 9ca0ea28..b5fdf3db 100644 --- a/modules/nf-core/agat/convertspgff2tsv/environment.yml +++ b/modules/nf-core/agat/convertspgff2tsv/environment.yml @@ -1,3 +1,4 @@ +name: agat_convertspgff2tsv channels: - conda-forge - bioconda diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml new file mode 100644 index 00000000..17a04ef2 --- /dev/null +++ b/modules/nf-core/cat/cat/environment.yml @@ -0,0 +1,7 @@ +name: cat_cat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 9f062219..4264a92c 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -2,7 +2,7 @@ process CAT_CAT { tag "$meta.id" label 'process_low' - conda "conda-forge::pigz=2.3.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : 'biocontainers/pigz:2.3.4' }" diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml index 8acc0bfa..00a8db0b 100644 --- a/modules/nf-core/cat/cat/meta.yml +++ b/modules/nf-core/cat/cat/meta.yml @@ -7,9 +7,7 @@ keywords: tools: - cat: description: Just concatenation - documentation: https://man7.org/linux/man-pages/man1/cat.1.html - licence: ["GPL-3.0-or-later"] input: - meta: @@ -21,7 +19,6 @@ input: type: file description: List of compressed / uncompressed files pattern: "*" - output: - versions: type: file @@ -31,7 +28,9 @@ output: type: file description: Concatenated file. Will be gzipped if file_out ends with ".gz" pattern: "${file_out}" - authors: - "@erikrikarddaniel" - "@FriederikeHanssen" +maintainers: + - "@erikrikarddaniel" + - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test new file mode 100644 index 00000000..5766daaf --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -0,0 +1,153 @@ +nextflow_process { + + name "Test Process CAT_CAT" + script "../main.nf" + process "CAT_CAT" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/cat" + + test("test_cat_unzipped_unzipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + + test("test_cat_zipped_zipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} + ) + } + } + + test("test_cat_zipped_unzipped") { + config './nextflow_zipped_unzipped.config' + + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_cat_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} + ) + } + } + + test("test_cat_one_file_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} + ) + } + } +} + diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap new file mode 100644 index 00000000..423571ba --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -0,0 +1,121 @@ +{ + "test_cat_unzipped_zipped_size": { + "content": [ + 375 + ], + "timestamp": "2023-10-16T14:33:08.049445686" + }, + "test_cat_unzipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:18.500464399" + }, + "test_cat_zipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:49.642741302" + }, + "test_cat_zipped_zipped_lines": { + "content": [ + [ + "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", + "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", + "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", + "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ] + ], + "timestamp": "2023-10-16T14:32:33.629048645" + }, + "test_cat_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:08.038830506" + }, + "test_cat_one_file_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:21.39642399" + }, + "test_cat_zipped_zipped_size": { + "content": [ + 78 + ], + "timestamp": "2023-10-16T14:32:33.641869244" + }, + "test_cat_one_file_unzipped_zipped_size": { + "content": [ + 374 + ], + "timestamp": "2023-10-16T14:33:21.4094373" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config new file mode 100644 index 00000000..ec26b0fd --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config @@ -0,0 +1,6 @@ + +process { + withName: CAT_CAT { + ext.prefix = 'cat.txt.gz' + } +} diff --git a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config new file mode 100644 index 00000000..fbc79783 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config @@ -0,0 +1,8 @@ + +process { + + withName: CAT_CAT { + ext.prefix = 'cat.txt' + } + +} diff --git a/modules/nf-core/cat/cat/tests/tags.yml b/modules/nf-core/cat/cat/tests/tags.yml new file mode 100644 index 00000000..37b578f5 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/tags.yml @@ -0,0 +1,2 @@ +cat/cat: + - modules/nf-core/cat/cat/** diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 00000000..bff93add --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,7 @@ +name: cat_fastq +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 5021e6fc..3d963784 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index 8a39e309..db4ac3c7 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -34,7 +34,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@joseespinosa" - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 00000000..f5f94182 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,143 @@ +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.reads).match() }, + { assert path(process.out.versions.get(0)).getText().contains("cat") } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 00000000..ec2342e5 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,78 @@ +{ + "test_cat_fastq_single_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d" + ] + ] + ], + "timestamp": "2023-10-17T23:19:12.990284837" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66" + ] + ] + ], + "timestamp": "2023-10-17T23:19:31.554568147" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,e325ef7deb4023447a1f074e285761af" + ] + ] + ], + "timestamp": "2023-10-17T23:19:49.629360033" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,63f817db7a29a03eb538104495556f66", + "test_2.merged.fastq.gz:md5,fe9f266f43a6fc3dcab690a18419a56e" + ] + ] + ] + ], + "timestamp": "2023-10-17T23:19:40.711617539" + }, + "test_cat_fastq_paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,f9cf5e375f7de81a406144a2c70cc64d", + "test_2.merged.fastq.gz:md5,77c8e966e130d8c6b6ec9be52fcb2bda" + ] + ] + ] + ], + "timestamp": "2023-10-18T07:53:20.923560211" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml new file mode 100644 index 00000000..6ac43614 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/tags.yml @@ -0,0 +1,2 @@ +cat/fastq: + - modules/nf-core/cat/fastq/** diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..f0c63f69 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..eec1db10 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..4274ed57 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,27 @@ +{ + "Should run without failures": { + "content": [ + { + "0": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ], + "1": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "2": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "mqc_yml": [ + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" + ], + "versions": [ + "versions.yml:md5,3843ac526e762117eedf8825b40683df" + ], + "yml": [ + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" + ] + } + ], + "timestamp": "2023-11-03T14:43:22.157011" + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml new file mode 100644 index 00000000..70389e66 --- /dev/null +++ b/modules/nf-core/fastp/environment.yml @@ -0,0 +1,7 @@ +name: fastp +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf index 831b7f12..c8e815ae 100644 --- a/modules/nf-core/fastp/main.nf +++ b/modules/nf-core/fastp/main.nf @@ -2,7 +2,7 @@ process FASTP { tag "$meta.id" label 'process_medium' - conda "bioconda::fastp=0.23.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastp:0.23.4--h5f740d0_0' : 'biocontainers/fastp:0.23.4--h5f740d0_0' }" diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 197ea7ca..c22a16ab 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -33,7 +33,6 @@ input: - save_merged: type: boolean description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz` - output: - meta: type: map @@ -71,3 +70,6 @@ output: authors: - "@drpatelh" - "@kevinmenden" +maintainers: + - "@drpatelh" + - "@kevinmenden" diff --git a/modules/nf-core/fastp/tests/main.nf.test b/modules/nf-core/fastp/tests/main.nf.test new file mode 100644 index 00000000..f610b735 --- /dev/null +++ b/modules/nf-core/fastp/tests/main.nf.test @@ -0,0 +1,485 @@ +nextflow_process { + + name "Test Process FASTP" + script "../main.nf" + process "FASTP" + tag "modules" + tag "modules_nfcore" + tag "fastp" + + test("test_fastp_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ + [ id:'test', single_end:true ], + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)" ] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("fastp test_fastp_interleaved") { + config './nextflow.config' + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = false + + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) ] + ] + + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "paired end (151 cycles + 151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 198"] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("fastp test_fastp_interleaved_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_single_end_trim_fail") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + + input[0] = [ [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:12.922000 K (92.984097%)", + "single end (151 cycles)"] + def log_text = [ "Q20 bases: 12922(92.9841%)", + "reads passed filter: 99" ] + def read_lines = [ "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1)).linesGzip.contains(read_line) } + } + }, + { failed_read_lines.each { failed_read_line -> + { assert path(process.out.reads_fail.get(0).get(1)).linesGzip.contains(failed_read_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { assert snapshot(process.out.json).match("test_fastp_single_end_trim_fail_json") }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_trim_fail") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = true + save_merged = false + + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "Q20 bases:25.719000 K (93.033098%)", + "The input has little adapter percentage (~0.000000%), probably it's trimmed before."] + def log_text = [ "No adapter detected for read1", + "Q30 bases: 12281(88.3716%)"] + def json_text = ['"passed_filter_reads": 198'] + def read1_lines = ["@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1", + "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT", + "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { failed_read2_lines.each { failed_read2_line -> + { assert path(process.out.reads_fail.get(0).get(1).get(1)).linesGzip.contains(failed_read2_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_merged") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = [] + save_trimmed_fail = false + save_merged = true + + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "
    "] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683'] + def read1_lines = [ "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("test_fastp_paired_end_merged_adapterlist") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + adapter_fasta = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta", checkIfExists: true) + save_trimmed_fail = false + save_merged = true + + input[0] = [ [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = adapter_fasta + input[2] = save_trimmed_fail + input[3] = save_merged + """ + } + } + + then { + def html_text = [ "
    "] + def log_text = [ "Merged and filtered:", + "total reads: 75", + "total bases: 13683"] + def json_text = ['"merged_and_filtered": {', '"total_reads": 75', '"total_bases": 13683',"--adapter_fasta"] + def read1_lines = ["@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1", + "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC", + "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE + { assert path(process.out.reads.get(0).get(1).get(0)).linesGzip.contains(read1_line) } + } + }, + { read2_lines.each { read2_line -> + { assert path(process.out.reads.get(0).get(1).get(1)).linesGzip.contains(read2_line) } + } + }, + { read_merged_lines.each { read_merged_line -> + { assert path(process.out.reads_merged.get(0).get(1)).linesGzip.contains(read_merged_line) } + } + }, + { html_text.each { html_part -> + { assert path(process.out.html.get(0).get(1)).getText().contains(html_part) } + } + }, + { json_text.each { json_part -> + { assert path(process.out.json.get(0).get(1)).getText().contains(json_part) } + } + }, + { log_text.each { log_part -> + { assert path(process.out.log.get(0).get(1)).getText().contains(log_part) } + } + }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } +} diff --git a/modules/nf-core/fastp/tests/main.nf.test.snap b/modules/nf-core/fastp/tests/main.nf.test.snap new file mode 100644 index 00000000..0fa68c7d --- /dev/null +++ b/modules/nf-core/fastp/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "fastp test_fastp_interleaved_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,168f516f7bd4b7b6c32da7cba87299a4" + ] + ] + ], + "timestamp": "2023-10-17T11:04:45.794175881" + }, + "test_fastp_single_end_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,c852d7a6dba5819e4ac8d9673bedcacc" + ] + ] + ], + "timestamp": "2023-10-17T11:04:10.566343705" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,48ffc994212fb1fc9f83a74fa69c9f02" + ] + ], + "timestamp": "2023-10-17T11:04:10.582076024" + }, + "test_fastp_single_end_trim_fail_json": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.fastp.json:md5,9a7ee180f000e8d00c7fb67f06293eb5" + ] + ] + ], + "timestamp": "2023-10-17T11:05:00.379878948" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastp/tests/nextflow.config b/modules/nf-core/fastp/tests/nextflow.config new file mode 100644 index 00000000..0f7849ad --- /dev/null +++ b/modules/nf-core/fastp/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + + withName: FASTP { + ext.args = "--interleaved_in" + } +} diff --git a/modules/nf-core/fastp/tests/tags.yml b/modules/nf-core/fastp/tests/tags.yml new file mode 100644 index 00000000..c1afcce7 --- /dev/null +++ b/modules/nf-core/fastp/tests/tags.yml @@ -0,0 +1,2 @@ +fastp: + - modules/nf-core/fastp/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..1787b38a --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..50e59f2b 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 3961de60..6437a144 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -1,13 +1,18 @@ nextflow_process { name "Test Process FASTQC" - script "modules/nf-core/fastqc/main.nf" + script "../main.nf" process "FASTQC" + tag "modules" + tag "modules_nfcore" tag "fastqc" test("Single-Read") { when { + params { + outdir = "$outputDir" + } process { """ input[0] = [ @@ -21,12 +26,16 @@ nextflow_process { } then { - assert process.success - assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" - assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") - assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + assertAll ( + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
    Mon 2 Oct 2023
    test.gz
    + // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" }, + { assert path(process.out.html.get(0).get(1)).getText().contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" } + ) } - } - } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..636a32ce --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,10 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-10-09T23:40:54+0000" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 00000000..7834294b --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml new file mode 100644 index 00000000..e7cb4280 --- /dev/null +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_bedtointervallist +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/main.nf b/modules/nf-core/gatk4/bedtointervallist/main.nf index 24968c38..88b24b1a 100644 --- a/modules/nf-core/gatk4/bedtointervallist/main.nf +++ b/modules/nf-core/gatk4/bedtointervallist/main.nf @@ -2,7 +2,7 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 83617a7c..187da885 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -46,3 +46,6 @@ output: authors: - "@kevinmenden" - "@ramprasadn" +maintainers: + - "@kevinmenden" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml new file mode 100644 index 00000000..db663e14 --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_createsequencedictionary +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index 3e4efdd9..b47ad162 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -2,7 +2,7 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index 9b8b8c89..f9d70be0 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -15,7 +15,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -38,3 +37,6 @@ output: authors: - "@maxulysse" - "@ramprasadn" +maintainers: + - "@maxulysse" + - "@ramprasadn" diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml new file mode 100644 index 00000000..9adad104 --- /dev/null +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -0,0 +1,8 @@ +name: gatk4_markduplicates +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 + - bioconda::samtools=1.17 diff --git a/modules/nf-core/gatk4/markduplicates/main.nf b/modules/nf-core/gatk4/markduplicates/main.nf index 59e52a3d..564b86d3 100644 --- a/modules/nf-core/gatk4/markduplicates/main.nf +++ b/modules/nf-core/gatk4/markduplicates/main.nf @@ -2,7 +2,7 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0': 'biocontainers/mulled-v2-d9e7bad0f7fbc8f4458d5c3ab7ffaaf0235b59fb:f857e2d6cc88d35580d01cf39e0959a68b83c1d9-0' }" diff --git a/modules/nf-core/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml index d3e75505..b0f09d4b 100644 --- a/modules/nf-core/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/gatk4/markduplicates/meta.yml @@ -7,16 +7,12 @@ keywords: - sort tools: - gatk4: - description: - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] - input: - meta: type: map @@ -35,7 +31,6 @@ input: type: file description: Fasta index file pattern: "*.{fai}" - output: - meta: type: map @@ -66,8 +61,11 @@ output: type: file description: Duplicate metrics file generated by GATK pattern: "*.{metrics.txt}" - authors: - "@ajodeh-juma" - "@FriederikeHanssen" - "@maxulysse" +maintainers: + - "@ajodeh-juma" + - "@FriederikeHanssen" + - "@maxulysse" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..d2a9f21a --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 65d7dd0d..2bbc3983 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..f1aa660e 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,5 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +13,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +30,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +52,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml new file mode 100644 index 00000000..5c85f872 --- /dev/null +++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml @@ -0,0 +1,7 @@ +name: picard_collectinsertsizemetrics +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::picard=3.1.0 diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf index 1d538fae..48e4d2ad 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf +++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTINSERTSIZEMETRICS { tag "$meta.id" label 'process_single' - conda "bioconda::picard=3.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' : + 'biocontainers/picard:3.1.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml index e611bdd4..efd5abe0 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml @@ -6,7 +6,6 @@ keywords: - insert - statistics - bam - tools: - "picard": description: "Java tools for working with NGS data in the BAM format" @@ -14,7 +13,6 @@ tools: documentation: "https://broadinstitute.github.io/picard/" tool_dev_url: "https://github.com/broadinstitute/picard" licence: "['MIT']" - input: - meta: type: map @@ -25,7 +23,6 @@ input: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" - output: - meta: type: map @@ -46,3 +43,5 @@ output: pattern: "*.txt" authors: - "@FerriolCalvet" +maintainers: + - "@FerriolCalvet" diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml new file mode 100644 index 00000000..8adda491 --- /dev/null +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -0,0 +1,8 @@ +name: picard_collectwgsmetrics +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::picard=3.1.0 + - r::r-base diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 1d59334c..67aa5b5e 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS { tag "$meta.id" label 'process_single' - conda "bioconda::picard=3.0.0 r::r-base" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' : + 'biocontainers/picard:3.1.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index 19906f08..5576ef92 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -68,3 +68,8 @@ authors: - "@flowuenne" - "@lassefolkersen" - "@ramprasadn" +maintainers: + - "@drpatelh" + - "@flowuenne" + - "@lassefolkersen" + - "@ramprasadn" diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 00000000..73badedb --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,7 @@ +name: samtools_faidx +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 59ed3088..3aa98822 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 957b25e5..e189af28 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -55,3 +55,7 @@ authors: - "@drpatelh" - "@ewels" - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 00000000..3c6f95b2 --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,7 @@ +name: samtools_index +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4b..256bd7c4 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 8bd2fa6f..01a4ee03 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -51,3 +51,7 @@ authors: - "@drpatelh" - "@ewels" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml new file mode 100644 index 00000000..508659f0 --- /dev/null +++ b/modules/nf-core/samtools/sort/environment.yml @@ -0,0 +1,7 @@ +name: samtools_sort +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 2b7753fd..60f0c634 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 07328431..2200de72 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -46,3 +46,6 @@ output: authors: - "@drpatelh" - "@ewels" +maintainers: + - "@drpatelh" + - "@ewels" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test new file mode 100644 index 00000000..1f72f3b9 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -0,0 +1,70 @@ +nextflow_process { + + name "Test Process SAMTOOLS_SORT" + script "../main.nf" + process "SAMTOOLS_SORT" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/sort" + + test("test_samtools_sort") { + + config "./nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + [ + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_samtools_sort_stub") { + + config "./nextflow.config" + options "-stub-run" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + [ + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..a43566da --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -0,0 +1,39 @@ +{ + "test_samtools_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,a29570e7607d217c2fa4d75829e09cd7" + ] + ], + "csi": [ + + ], + "versions": [ + "versions.yml:md5,46f7a36082fa1f68285fe30d689244e8" + ] + } + ], + "timestamp": "2023-10-17T17:21:46.5427968" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/tests/nextflow.config b/modules/nf-core/samtools/sort/tests/nextflow.config new file mode 100644 index 00000000..d0f35086 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_SORT { + ext.prefix = { "${meta.id}.sorted" } + } + +} diff --git a/modules/nf-core/samtools/sort/tests/tags.yml b/modules/nf-core/samtools/sort/tests/tags.yml new file mode 100644 index 00000000..cd63ea20 --- /dev/null +++ b/modules/nf-core/samtools/sort/tests/tags.yml @@ -0,0 +1,3 @@ +samtools/sort: + - modules/nf-core/samtools/sort/** + - tests/modules/nf-core/samtools/sort/** diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml new file mode 100644 index 00000000..141e7bd8 --- /dev/null +++ b/modules/nf-core/samtools/view/environment.yml @@ -0,0 +1,7 @@ +name: samtools_view +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index cb91facf..ddf3f88a 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 3b05450b..3dadafae 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -82,3 +82,8 @@ authors: - "@joseespinosa" - "@FriederikeHanssen" - "@priyanka-surana" +maintainers: + - "@drpatelh" + - "@joseespinosa" + - "@FriederikeHanssen" + - "@priyanka-surana" diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml new file mode 100644 index 00000000..6db20988 --- /dev/null +++ b/modules/nf-core/star/align/environment.yml @@ -0,0 +1,9 @@ +name: star_align +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::star=2.7.10a + - bioconda::samtools=1.16.1 + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index d0e20384..fa645a6d 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN { tag "$meta.id" label 'process_high' - conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index 3d8fed0c..e80dbb7d 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -52,7 +52,6 @@ input: - seq_center: type: string description: Sequencing center - output: - bam: type: file @@ -106,8 +105,11 @@ output: type: file description: STAR output bedGraph format file(s) (optional) pattern: "*.bg" - authors: - "@kevinmenden" - "@drpatelh" - "@praveenraj2018" +maintainers: + - "@kevinmenden" + - "@drpatelh" + - "@praveenraj2018" diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml new file mode 100644 index 00000000..0b35ff51 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -0,0 +1,9 @@ +name: star_genomegenerate +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::star=2.7.10a + - bioconda::samtools=1.16.1 + - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 43424042..473e62a6 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE { tag "$fasta" label 'process_high' - conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index eba2d9cf..1061e1b8 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -31,7 +31,6 @@ input: - gtf: type: file description: GTF file of the reference genome - output: - meta: type: map @@ -46,7 +45,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@kevinmenden" - "@drpatelh" +maintainers: + - "@kevinmenden" + - "@drpatelh" diff --git a/modules/nf-core/stringtie/merge/environment.yml b/modules/nf-core/stringtie/merge/environment.yml new file mode 100644 index 00000000..9914b202 --- /dev/null +++ b/modules/nf-core/stringtie/merge/environment.yml @@ -0,0 +1,7 @@ +name: stringtie_merge +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/stringtie/merge/main.nf b/modules/nf-core/stringtie/merge/main.nf index 12224f78..c2568219 100644 --- a/modules/nf-core/stringtie/merge/main.nf +++ b/modules/nf-core/stringtie/merge/main.nf @@ -2,7 +2,7 @@ process STRINGTIE_MERGE { label 'process_medium' // Note: 2.7X indices incompatible with AWS iGenomes. - conda "bioconda::stringtie=2.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : 'biocontainers/stringtie:2.2.1--hecb563c_2' }" diff --git a/modules/nf-core/stringtie/merge/meta.yml b/modules/nf-core/stringtie/merge/meta.yml index 2e9784fe..5d02d678 100644 --- a/modules/nf-core/stringtie/merge/meta.yml +++ b/modules/nf-core/stringtie/merge/meta.yml @@ -32,6 +32,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@yuukiiwa" +maintainers: + - "@yuukiiwa" diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml new file mode 100644 index 00000000..7a0eccdb --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -0,0 +1,7 @@ +name: stringtie_stringtie +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index d0f8b563..6e25ba27 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -2,7 +2,7 @@ process STRINGTIE_STRINGTIE { tag "$meta.id" label 'process_medium' - conda "bioconda::stringtie=2.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : 'biocontainers/stringtie:2.2.1--hecb563c_2' }" diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml index 75518470..d8ebdd88 100644 --- a/modules/nf-core/stringtie/stringtie/meta.yml +++ b/modules/nf-core/stringtie/stringtie/meta.yml @@ -5,7 +5,6 @@ keywords: - assembly - quantification - gtf - tools: - stringtie2: description: | @@ -55,3 +54,5 @@ output: pattern: "versions.yml" authors: - "@drpatelh" +maintainers: + - "@drpatelh" From ef9f57a869e79446397e22c260aa9c80cab962ab Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 15 Nov 2023 10:40:39 +0100 Subject: [PATCH 219/264] move compression out of vcf_collect --- bin/vcf_collect.py | 5 ++--- modules/local/vcf_collect/main.nf | 3 ++- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 4d677de0..8e15ccfc 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -8,7 +8,6 @@ import ast import numpy as np import csv -import gzip logger = logging.getLogger() @@ -344,9 +343,9 @@ def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: "FORMAT", "Sample", ] - ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE, compression="gzip") + ].to_csv(path_or_buf=out_file, sep="\t", header=None, index=False, quoting=csv.QUOTE_NONE) - with gzip.open(out_file, "r+") as f: + with open(out_file, "r+") as f: content = f.read() f.seek(0, 0) f.write(header.rstrip("\r\n") + "\n" + content) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index 42f94c40..1b8e56fe 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -22,7 +22,8 @@ process VCF_COLLECT { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf.gz + vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf + gzip ${prefix}_fusion_data.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": From f33a5e9f36271d07c11cb28b762a2c3859aa7302 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 15 Nov 2023 13:25:59 +0100 Subject: [PATCH 220/264] fix ,/; --- bin/vcf_collect.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 8e15ccfc..57cfbcaa 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -319,7 +319,7 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: f"TRANSCRIPT_ID_A={row['CDS_LEFT_ID']};TRANSCRIPT_ID_B={row['CDS_RIGHT_ID']};" f"TRANSCRIPT_VERSION_A={row['Left_transcript_version']};TRANSCRIPT_VERSION_B={row['Right_transcript_version']};" f"HGNC_ID_A={row['Left_hgnc_id']};HGNC_ID_B={row['Right_hgnc_id']};" - f"EXON_NUMBER_A={row['Left_exon_number']},EXON_NUMBER_B={row['Right_exon_number']};" + f"EXON_NUMBER_A={row['Left_exon_number']};EXON_NUMBER_B={row['Right_exon_number']};" f"ANNOTATIONS={row['annots']}" ) df.loc[index, "Sample"] = f"./1:{row['JunctionReadCount']}:{row['SpanningFragCount']}:{row['FFPM']}" From a8b07438c70907de25960cfbf934e1b175e82cd2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 16 Nov 2023 21:35:59 +0100 Subject: [PATCH 221/264] fix values display vcf --- bin/vcf_collect.py | 13 ++++++++++++- modules/local/vcf_collect/main.nf | 2 +- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 57cfbcaa..dbbd384e 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -275,7 +275,7 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: concatenate_columns, axis=1 ) fusion_report.columns = fusion_report.columns.str.upper() - fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply(lambda x: ", ".join(x)) + fusion_report["FOUND_DB"] = fusion_report["FOUND_DB"].apply(lambda x: ",".join(x)) fusion_report[["GeneA", "GeneB"]] = fusion_report["FUSION"].str.split("--", expand=True) return fusion_report[["FUSION", "GeneA", "GeneB", "TOOLS_HITS", "SCORE", "FOUND_DB", "FOUND_IN"]].set_index( @@ -297,6 +297,17 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: df["INFO"] = "" df["Sample"] = "" df["Strand1"] = df["Strand1"].astype(str) + df["JunctionReadCount"] = df["JunctionReadCount"].fillna(0).astype(int).astype(str) + df["SpanningFragCount"] = df["SpanningFragCount"].fillna(0).astype(int).astype(str) + df["FFPM"] = df["FFPM"].fillna(0).astype(float).astype(str) + df["ChromosomeA"] = df["ChromosomeA"].fillna(0).astype(int).astype(str) + df["ChromosomeB"] = df["ChromosomeB"].fillna(0).astype(int).astype(str) + df["Left_hgnc_id"] = df["Left_hgnc_id"].fillna(0).astype(int).astype(str) + df["Right_hgnc_id"] = df["Right_hgnc_id"].fillna(0).astype(int).astype(str) + df["Left_exon_number"] = df["Left_exon_number"].fillna(0).astype(int).astype(str) + df["Right_exon_number"] = df["Right_exon_number"].fillna(0).astype(int).astype(str) + df["Left_transcript_version"] = df["Left_transcript_version"].fillna(0).astype(int).astype(str) + df["Right_transcript_version"] = df["Right_transcript_version"].fillna(0).astype(int).astype(str) for index, row in df.iterrows(): if row["Strand1"] == "nan": diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index 1b8e56fe..2af4a777 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -2,7 +2,7 @@ process VCF_COLLECT { tag "$meta.id" label 'process_single' - conda "conda-forge::python=3.8.3" + conda "conda-forge::pandas=1.5.2" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pandas:1.5.2' : 'quay.io/biocontainers/pandas:1.5.2' }" From acf64a1d862a7c16fd68d6bd736100e1c1c4ae1c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 17 Nov 2023 13:54:11 +0100 Subject: [PATCH 222/264] add hgnc id for fusionreport-only entries in vcf and add bug fix --- bin/vcf_collect.py | 44 +++++++++++++++++++++++++++++++++----------- 1 file changed, 33 insertions(+), 11 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index dbbd384e..b5ff126d 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -37,19 +37,36 @@ def vcf_collect( .join(read_build_fusionreport(fusionreport_in_file), how="outer", on="FUSION") .reset_index() ) + hgnc_df = build_hgnc_dataframe(hgnc) - df = build_hgcn_dataframe(hgnc).merge( - merged_df, how="right", left_on="ensembl_gene_id", right_on="Left_ensembl_gene_id" + df_symbol = merged_df[merged_df["Left_ensembl_gene_id"].isna()] + df_not_symbol = merged_df[merged_df["Left_ensembl_gene_id"].notna()] + + df_not_symbol = hgnc_df.merge( + df_not_symbol, how="right", left_on="ensembl_gene_id", right_on="Left_ensembl_gene_id" ) + df_symbol = hgnc_df.merge(df_symbol, how="right", left_on="symbol", right_on="GeneA") + df = pd.concat([df_not_symbol, df_symbol]) df = df.rename(columns={"hgnc_id": "Left_hgnc_id"}) - df = build_hgcn_dataframe(hgnc).merge(df, how="right", left_on="ensembl_gene_id", right_on="Right_ensembl_gene_id") + + df_symbol = df[df["Right_ensembl_gene_id"].isna()] + df_not_symbol = df[df["Right_ensembl_gene_id"].notna()] + + df_not_symbol = hgnc_df.merge( + df_not_symbol, how="right", left_on="ensembl_gene_id", right_on="Right_ensembl_gene_id" + ) + df_symbol = hgnc_df.merge(df_symbol, how="right", left_on="symbol", right_on="GeneB") + df = pd.concat([df_not_symbol, df_symbol]) df = df.rename(columns={"hgnc_id": "Right_hgnc_id"}) + gtf_df = build_gtf_dataframe(gtf) all_df = df.merge(gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id") - all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].fillna(0) - all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].astype(int) + all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].fillna(0).astype(int) - all_df = all_df[(all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])] + all_df = all_df[ + ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) + | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) + ] all_df = all_df.rename(columns={"transcript_version": "Left_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Left_exon_number"}) all_df = all_df[ @@ -83,10 +100,14 @@ def vcf_collect( all_df = all_df.merge(gtf_df, how="left", left_on="CDS_RIGHT_ID", right_on="Transcript_id") all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].fillna(0) all_df[["PosB", "orig_start", "orig_end"]] = all_df[["PosB", "orig_start", "orig_end"]].astype(int) - all_df = all_df[(all_df["PosB"] >= all_df["orig_start"]) & (all_df["PosB"] <= all_df["orig_end"])] + all_df = all_df[ + ((all_df["PosB"] >= all_df["orig_start"]) & (all_df["PosB"] <= all_df["orig_end"])) + | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) + ] all_df = all_df.rename(columns={"transcript_version": "Right_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Right_exon_number"}) + all_df = all_df[ [ "FUSION", @@ -300,8 +321,8 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: df["JunctionReadCount"] = df["JunctionReadCount"].fillna(0).astype(int).astype(str) df["SpanningFragCount"] = df["SpanningFragCount"].fillna(0).astype(int).astype(str) df["FFPM"] = df["FFPM"].fillna(0).astype(float).astype(str) - df["ChromosomeA"] = df["ChromosomeA"].fillna(0).astype(int).astype(str) - df["ChromosomeB"] = df["ChromosomeB"].fillna(0).astype(int).astype(str) + df["ChromosomeA"] = df["ChromosomeA"].fillna(0).astype(str) + df["ChromosomeB"] = df["ChromosomeB"].fillna(0).astype(str) df["Left_hgnc_id"] = df["Left_hgnc_id"].fillna(0).astype(int).astype(str) df["Right_hgnc_id"] = df["Right_hgnc_id"].fillna(0).astype(int).astype(str) df["Left_exon_number"] = df["Left_exon_number"].fillna(0).astype(int).astype(str) @@ -334,6 +355,7 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: f"ANNOTATIONS={row['annots']}" ) df.loc[index, "Sample"] = f"./1:{row['JunctionReadCount']}:{row['SpanningFragCount']}:{row['FFPM']}" + return df @@ -362,13 +384,13 @@ def write_vcf(df_to_print: pd.DataFrame, header: str, out_file: str) -> None: f.write(header.rstrip("\r\n") + "\n" + content) -def build_hgcn_dataframe(file: str) -> pd.DataFrame: +def build_hgnc_dataframe(file: str) -> pd.DataFrame: """ Build a DataFrame from HGNC input file, extracting 'hgnc_id' and 'ensembl_gene_id' columns. """ df = pd.read_csv(file, sep="\t", low_memory=False) df["hgnc_id"] = df["hgnc_id"].str.replace("HGNC:", "") - return df[["hgnc_id", "ensembl_gene_id"]].dropna() + return df[["hgnc_id", "ensembl_gene_id", "symbol"]].dropna() def build_gtf_dataframe(file: str) -> pd.DataFrame: From 1f872d4223508dd04ebb8d5585322967df04ad37 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 20 Nov 2023 09:44:01 +0100 Subject: [PATCH 223/264] add info on fusionreport scoring, genome supported, tool_cutoff and arriba visualisation --- docs/output.md | 19 +++++++++++++++++-- docs/usage.md | 8 +++++++- 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/docs/output.md b/docs/output.md index 584ed5b6..4056c6aa 100644 --- a/docs/output.md +++ b/docs/output.md @@ -118,6 +118,8 @@ If no parameters are specified, the default is applied.
    +The visualisation displays the fusions that fusioninspector outputs. That means that fusions from all callers are aggregated (by fusion-report) and then analyzed through fusioninspector (Note: Fusioninspecor contains a filtering step!). + ### Cat
    @@ -216,9 +218,22 @@ Please note that fusion-report is executed from fork https://github.com/Clinical
    [Fusion-report](https://github.com/matq007/fusion-report) is a tool for parsing outputs from fusion detection tools. -The score is explained [on the original fusion-report github page](https://matq007.github.io/fusion-report/#/score). +The score is explained here: . Summary: + +The weights for databases are as follows: + +* FusionGDB (20) +* COSMIC (40) +* MITELMAN (40) +* FusionGDB2 (0) + +The final formula for calculating score is: + +$$ +score = 0.5 * \sum_{tool}^{tools} f(fusion, tool)*w(tool) + 0.5 * \sum_{db}^{dbs} g(fusion, db)*w(db) +$$ -`--fusionreport_filter` can be used to filter the output of fusion-report to fusions identified by at least 2 different tools. +All tools have the same weight. ### Kallisto diff --git a/docs/usage.md b/docs/usage.md index 90725471..c4b0359d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -184,6 +184,12 @@ outdir: './results/' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). + +:::warning +Conda is not currently supported. +Supported genome is currently only GRCh38. +::: + ### Options #### Trimming @@ -212,7 +218,7 @@ nextflow run nf-core/rnafusion \ --tools_cutoff ``` -`--tools_cutoff INT` will discard fusions detected by less than INT tools both for display in fusionreport html index and to consider in fusioninspector. +`--tools_cutoff INT` will discard fusions detected by less than INT tools both for display in fusionreport html index and to consider in fusioninspector. Default = 1, no filtering. #### Adding custom fusions to consider as well as the detected set: whitelist From 5fb4b5700eb71278177b5917836c24b0761ceddd Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 20 Nov 2023 09:53:16 +0100 Subject: [PATCH 224/264] improve documentation --- docs/output.md | 2 ++ docs/usage.md | 13 +++++++++++++ 2 files changed, 15 insertions(+) diff --git a/docs/output.md b/docs/output.md index 2a55052a..1bf58249 100644 --- a/docs/output.md +++ b/docs/output.md @@ -255,6 +255,8 @@ Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or - `vcf_collect` - `_fusion_data.vcf` - contains the fusions in vcf format with collected statistics. +Vcf-collect takes as input the results of fusion-report and fusioninspector. That means fusions from all tools are aggregated. Fusioninspector applies a filter so it is possible some fusions detected by a caller are not filtered out by fusioninspector. In those cases, vcf-collect will display the fusions, but a lot of data will be missing as fusioninspector performs the analysis for each fusion. +
    [Megafusion](https://github.com/J35P312/MegaFusion) converts RNA fusion files to SV VCF and collects statistics and metrics in a VCF file. diff --git a/docs/usage.md b/docs/usage.md index 1f651fd5..c97942c9 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -299,6 +299,19 @@ Use the parameter `--cram` to compress the BAM files to CRAM for specific tools. - `--cram arriba,starfusion`, default: [] - `--cram arriba` +### Troubleshooting + +#### GstrandBit issues + +The issue below sometimes occurs: + +``` +EXITING because of FATAL ERROR: cannot insert sequence on the fly because of strand GstrandBit problem +SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star +``` + +As the error message suggest, it is a STAR-related error and your best luck in solving it will be the forum. + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: From 5389e7692e4806ee3fd9170773de4647d40a9ed2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 20 Nov 2023 10:42:17 +0100 Subject: [PATCH 225/264] prettier --- docs/output.md | 8 ++++---- docs/usage.md | 1 - 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/output.md b/docs/output.md index 1bf58249..559e5fb2 100644 --- a/docs/output.md +++ b/docs/output.md @@ -222,10 +222,10 @@ The score is explained here: Date: Mon, 20 Nov 2023 13:20:41 +0100 Subject: [PATCH 226/264] Update docs/usage.md Co-authored-by: Peter Pruisscher <57712924+peterpru@users.noreply.github.com> --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 494ddfab..b3625332 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -309,7 +309,7 @@ EXITING because of FATAL ERROR: cannot insert sequence on the fly because of str SOLUTION: please contact STAR author at https://groups.google.com/forum/#!forum/rna-star ``` -As the error message suggest, it is a STAR-related error and your best luck in solving it will be the forum. +As the error message suggests, it is a STAR-related error and your best luck in solving it will be the forum. ### Updating the pipeline From 9d7b98a0988e32968981e212f1f233b07229bcdf Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 20 Nov 2023 16:49:29 +0100 Subject: [PATCH 227/264] Fill non-empty values within each group for 'exon_number' and 'transcript_version' --- bin/vcf_collect.py | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index b5ff126d..5d359107 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -63,10 +63,24 @@ def vcf_collect( all_df = df.merge(gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id") all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].fillna(0).astype(int) + all_df["bla"] = ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) | ( + (all_df["orig_start"] == 0) & (all_df["orig_end"] == 0) + ) + all_df = all_df[ ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) ] + + all_df.replace("", np.nan, inplace=True) + # Fill non-empty values within each group for 'exon_number' and 'transcript_version' + all_df["exon_number"] = all_df.groupby("PosA")["exon_number"].transform( + lambda x: x.fillna(method="ffill").fillna(method="bfill") + ) + all_df["transcript_version"] = all_df.groupby("PosA")["transcript_version"].transform( + lambda x: x.fillna(method="ffill").fillna(method="bfill") + ) + all_df = all_df.rename(columns={"transcript_version": "Left_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Left_exon_number"}) all_df = all_df[ From 6fe7cdd43607f71f3fe4d536086c29519478b319 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 20 Nov 2023 16:53:32 +0100 Subject: [PATCH 228/264] remove max_sensitivity and max_mate_dist from fusioninspector filtering --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 39135aa3..61535a7e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -94,7 +94,7 @@ process { withName: FUSIONINSPECTOR { ext.when = { !params.skip_vis } ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' } - ext.args2 = '--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect' + ext.args2 = '--annotate --examine_coding_effect' } withName: FUSIONREPORT { From 0b2e62a5c5613735d4ca0c279d34db653e2d315d Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 20 Nov 2023 17:29:47 +0100 Subject: [PATCH 229/264] add fastp output and fastqc after trim to multiqc --- assets/multiqc_config.yaml | 30 ------------------------------ assets/multiqc_config.yml | 23 +++++++++++++++++++++++ 2 files changed, 23 insertions(+), 30 deletions(-) delete mode 100644 assets/multiqc_config.yaml diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml deleted file mode 100644 index 61602fc9..00000000 --- a/assets/multiqc_config.yaml +++ /dev/null @@ -1,30 +0,0 @@ -custom_logo: "nf-core-rnafusion_logo_light.png" -custom_logo_url: https://github.com/nf-core/rnafusion -custom_logo_title: "nf-core/rnafusion" - -report_comment: > - This report has been generated by the nf-core/rnafusion - analysis pipeline. For information about how to interpret these results, please see the - documentation. -report_section_order: - "nf-core-rnafusion-methods-description": - order: -1000 - software_versions: - order: -1001 - "nf-core-rnafusion-summary": - order: -1002 - -export_plots: true - -run_modules: - - fastqc - - picard - - fastp - - gatk - - star - -module_order: - - fastqc: - name: "FastQC" - path_filters: - - "*.zip" diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 40a09e62..bce891ff 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -10,3 +10,26 @@ report_section_order: order: -1001 export_plots: true + +# Run only these modules +run_modules: + - custom_content + - fastqc + - fastp + - star + - samtools + - picard + + +module_order: + - fastqc: + name: "FastQC (raw)" + info: "This section of the report shows FastQC results before adapter trimming." + path_filters: + - "./fastqc/raw/*.zip" + - fastp + - fastqc: + name: "FastQC (trimmed)" + info: "This section of the report shows FastQC results after adapter trimming." + path_filters: + - "./fastqc/trim/*.zip" From 311e1abe8f9acf4a97d7e534f4474ec80d9eb1ff Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 13:47:38 +0100 Subject: [PATCH 230/264] fix multiqx --- assets/multiqc_config.yml | 11 +++++++---- conf/modules.config | 5 +++++ workflows/rnafusion.nf | 3 +++ 3 files changed, 15 insertions(+), 4 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index bce891ff..1683ee24 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -4,10 +4,12 @@ report_comment: > documentation. report_section_order: - software_versions: + nf-core-rnafusion-methods-description: order: -1000 - nf-core-rnafusion-summary: + software_versions: order: -1001 + nf-core-rnafusion-summary: + order: -1002 export_plots: true @@ -19,6 +21,7 @@ run_modules: - star - samtools - picard + - arriba module_order: @@ -26,10 +29,10 @@ module_order: name: "FastQC (raw)" info: "This section of the report shows FastQC results before adapter trimming." path_filters: - - "./fastqc/raw/*.zip" + - "./fastqc/*.zip" - fastp - fastqc: name: "FastQC (trimmed)" info: "This section of the report shows FastQC results after adapter trimming." path_filters: - - "./fastqc/trim/*.zip" + - "./fastqc_for_trim/*.zip" diff --git a/conf/modules.config b/conf/modules.config index 61535a7e..962bb1e9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -68,6 +68,11 @@ process { withName: FASTQC { ext.args = '--quiet' ext.when = { !params.skip_qc } + publishDir = [ + path: { "${params.outdir}/fastqc" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] } withName: FASTQC_FOR_TRIM { diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 6792eff8..78133922 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -263,6 +263,9 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.html.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FOR_FASTP.out.zip.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([])) From de83a08d9e47e4f833a58bef6db0f4983d49d22f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 13:58:24 +0100 Subject: [PATCH 231/264] add files to multiqc --- assets/multiqc_config.yml | 5 +++++ subworkflows/local/fusioninspector_workflow.nf | 5 ++++- subworkflows/local/starfusion_workflow.nf | 3 +++ workflows/rnafusion.nf | 2 ++ 4 files changed, 14 insertions(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 1683ee24..886ceef0 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -36,3 +36,8 @@ module_order: info: "This section of the report shows FastQC results after adapter trimming." path_filters: - "./fastqc_for_trim/*.zip" + - arriba: + name: "Arriba visualisation" + info: "This section of the report shows Arriba visualisation after FusionInspector analysis." + path_filters: + - "./arriba_visualisation/*.pdf" diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 32173e81..3f1f9f13 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -19,6 +19,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { main: ch_versions = Channel.empty() + ch_arriba_visualisation = Channel.empty() index ="${params.starfusion_ref}" ch_fusion_list = ( params.tools_cutoff > 1 ? fusion_list_filtered : fusion_list ) @@ -53,9 +54,11 @@ workflow FUSIONINSPECTOR_WORKFLOW { ch_bam_sorted_indexed_fusions = bam_sorted_indexed.join(FUSIONINSPECTOR.out.tsv) ARRIBA_VISUALISATION(ch_bam_sorted_indexed_fusions, ch_gtf, ch_arriba_ref_protein_domains, ch_arriba_ref_cytobands) ch_versions = ch_versions.mix(ARRIBA_VISUALISATION.out.versions) + ch_arriba_visualisation = ARRIBA_VISUALISATION.out.pdf } emit: - versions = ch_versions.ifEmpty(null) + arriba_visualisation = ch_arriba_visualisation.ifEmpty(null) + versions = ch_versions.ifEmpty(null) } diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf index 2c3a118e..38264c01 100644 --- a/subworkflows/local/starfusion_workflow.nf +++ b/subworkflows/local/starfusion_workflow.nf @@ -45,16 +45,19 @@ workflow STARFUSION_WORKFLOW { ch_starfusion_fusions = STARFUSION.out.fusions ch_star_stats = STAR_FOR_STARFUSION.out.log_final + ch_star_gene_count = STAR_FOR_STARFUSION.out.read_per_gene_tab } } else { ch_starfusion_fusions = reads.combine(Channel.value(file(ch_dummy_file, checkIfExists:true))) .map { meta, reads, fusions -> [ meta, fusions ] } ch_star_stats = Channel.empty() + ch_star_gene_count = Channel.empty() } emit: fusions = ch_starfusion_fusions star_stats = ch_star_stats + star_gene_count = ch_star_gene_count ch_bam_sorted = ch_align.ifEmpty([[],[]]) ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty([[],[],[]]) versions = ch_versions.ifEmpty(null) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 78133922..cd223444 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -267,9 +267,11 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FOR_FASTP.out.zip.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_gene_count.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.arriba_visualisation.collect{it[1]}.ifEmpty([])) From 45505e75a471e826e7f99bd6d190a8f8cbaebb6a Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 14:00:36 +0100 Subject: [PATCH 232/264] prettier --- assets/multiqc_config.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 886ceef0..7e090b4a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -23,7 +23,6 @@ run_modules: - picard - arriba - module_order: - fastqc: name: "FastQC (raw)" From 3641a361edc075669f7dfbb73b0147c183fe9263 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 14:08:19 +0100 Subject: [PATCH 233/264] modules update + fix channel io --- modules.json | 4 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 6 +- modules/nf-core/multiqc/tests/main.nf.test | 91 +++++++++++++++++++ modules/nf-core/multiqc/tests/tags.yml | 2 + .../samtools/index/tests/csi.nextflow.config | 7 ++ .../nf-core/samtools/index/tests/main.nf.test | 87 ++++++++++++++++++ .../samtools/index/tests/main.nf.test.snap | 28 ++++++ modules/nf-core/samtools/index/tests/tags.yml | 2 + subworkflows/local/trim_workflow.nf | 9 ++ workflows/rnafusion.nf | 6 +- 11 files changed, 236 insertions(+), 8 deletions(-) create mode 100644 modules/nf-core/multiqc/tests/main.nf.test create mode 100644 modules/nf-core/multiqc/tests/tags.yml create mode 100644 modules/nf-core/samtools/index/tests/csi.nextflow.config create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test create mode 100644 modules/nf-core/samtools/index/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/index/tests/tags.yml diff --git a/modules.json b/modules.json index 724634dc..d13e5998 100644 --- a/modules.json +++ b/modules.json @@ -57,7 +57,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "214d575774c172062924ad3564b4f66655600730", + "git_sha": "1537442a7be4a78efa3d1ff700a923c627bbda5d", "installed_by": ["modules"] }, "picard/collectinsertsizemetrics": { @@ -77,7 +77,7 @@ }, "samtools/index": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8", "installed_by": ["modules"] }, "samtools/sort": { diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index d2a9f21a..bc0bdb5b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.17 + - bioconda::multiqc=1.18 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 2bbc3983..00cc48d2 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : - 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.18--pyhdfd78af_0' : + 'biocontainers/multiqc:1.18--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..68fffa90 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,91 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("MULTIQC: FASTQC") { + + setup { + run("FASTQC") { + script "../../fastqc/main.nf" + process { + """ + input[0] = Channel.of([ + [ id: 'test', single_end: false ], + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = FASTQC.out.zip.collect { it[1] } + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } + + test("MULTIQC: FASTQC and a config file") { + + setup { + run("FASTQC") { + script "../../fastqc/main.nf" + process { + """ + input[0] = Channel.of([ + [ id: 'test', single_end: false ], + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = FASTQC.out.zip.collect { it[1] } + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.report.get(0)).exists() }, + { assert path(process.out.data.get(0)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("multiqc") } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 00000000..0ed260ef --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 00000000..c76a9169 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("sarscov2 [BAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.bai).match("bai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CRAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.crai).match("crai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CSI]") { + + config "./csi.nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 00000000..b3baee7f --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "crai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ] + ], + "timestamp": "2023-11-15T15:17:37.30801" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ] + ], + "timestamp": "2023-11-15T15:17:30.869234" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 00000000..e0f58a7a --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf index 63012680..ef80ba32 100644 --- a/subworkflows/local/trim_workflow.nf +++ b/subworkflows/local/trim_workflow.nf @@ -9,6 +9,9 @@ workflow TRIM_WORKFLOW { main: ch_versions = Channel.empty() + ch_fastp_html = Channel.empty() + ch_fastp_json = Channel.empty() + ch_fastqc_trimmed = Channel.empty if (params.fastp_trim) { FASTP(reads, params.adapter_fasta, false, false) @@ -19,6 +22,9 @@ workflow TRIM_WORKFLOW { ch_reads_all = FASTP.out.reads ch_reads_fusioncatcher = ch_reads_all + ch_fastp_html = FASTP.out.html + ch_fastp_json = FASTP.out.json + ch_fastqc_trimmed = FASTQC_FOR_FASTP.out.zip } else { @@ -29,6 +35,9 @@ workflow TRIM_WORKFLOW { emit: ch_reads_all ch_reads_fusioncatcher + ch_fastp_html + ch_fastp_json + ch_fastqc_trimmed versions = ch_versions.ifEmpty(null) } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index cd223444..0cb60d60 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -263,9 +263,9 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.html.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.json.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC_FOR_FASTP.out.zip.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_html.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastp_json.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(TRIM_WORKFLOW.out.ch_fastqc_trimmed.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(STARFUSION_WORKFLOW.out.star_gene_count.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) From 4459e7c5997c426699db802359f8e3955f398a2e Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 14:13:47 +0100 Subject: [PATCH 234/264] fix typo --- subworkflows/local/trim_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf index ef80ba32..ce5244f1 100644 --- a/subworkflows/local/trim_workflow.nf +++ b/subworkflows/local/trim_workflow.nf @@ -11,7 +11,7 @@ workflow TRIM_WORKFLOW { ch_versions = Channel.empty() ch_fastp_html = Channel.empty() ch_fastp_json = Channel.empty() - ch_fastqc_trimmed = Channel.empty + ch_fastqc_trimmed = Channel.empty() if (params.fastp_trim) { FASTP(reads, params.adapter_fasta, false, false) From 5087346bb3d3cf9720489a79500b690f55ee9ce8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 14:23:47 +0100 Subject: [PATCH 235/264] fix --- subworkflows/local/fusioninspector_workflow.nf | 2 +- workflows/rnafusion.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 3f1f9f13..30f18596 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -58,7 +58,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { } emit: - arriba_visualisation = ch_arriba_visualisation.ifEmpty(null) + ch_arriba_visualisation versions = ch_versions.ifEmpty(null) } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 0cb60d60..fbf36b31 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -271,7 +271,7 @@ workflow RNAFUSION { ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]}.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.arriba_visualisation.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.ch_arriba_visualisation.collect{it[1]}.ifEmpty([])) From ba1f4e2fbdb4db09b9e53f7befd9c9644d4516f8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 15:20:46 +0100 Subject: [PATCH 236/264] fist steps --- bin/vcf_collect.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index b5ff126d..e83204c9 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -158,7 +158,13 @@ def parse_args(argv=None): "--fusionreport", metavar="FUSIONREPORT", type=Path, - help="Fusionreport output in TSV format.", + help="Fusionreport output in index/html format.", + ) + parser.add_argument( + "--fusionreport_csv", + metavar="FUSIONREPORT_CSV", + type=Path, + help="Fusionreport output in CSV format.", ) parser.add_argument( "--fusioninspector_gtf", @@ -303,6 +309,11 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: ["FUSION"] ) +def read_fusionreport_csv(file: str) -> pd.DataFrame: + df = pd.read_csv(file, sep="\t") + + + def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: """ From bccdbc1dc6463e5b65bb81e74ad0d42d71292471 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 15:38:27 +0100 Subject: [PATCH 237/264] fix paths --- assets/multiqc_config.yml | 6 +++--- conf/modules.config | 4 ++-- subworkflows/local/trim_workflow.nf | 1 - 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 7e090b4a..b21e8548 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -28,15 +28,15 @@ module_order: name: "FastQC (raw)" info: "This section of the report shows FastQC results before adapter trimming." path_filters: - - "./fastqc/*.zip" + - "*.zip" - fastp - fastqc: name: "FastQC (trimmed)" info: "This section of the report shows FastQC results after adapter trimming." path_filters: - - "./fastqc_for_trim/*.zip" + - "*.zip" - arriba: name: "Arriba visualisation" info: "This section of the report shows Arriba visualisation after FusionInspector analysis." path_filters: - - "./arriba_visualisation/*.pdf" + - "*.pdf" diff --git a/conf/modules.config b/conf/modules.config index 962bb1e9..ef3e69ab 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -75,10 +75,10 @@ process { ] } - withName: FASTQC_FOR_TRIM { + withName: FASTQC_FOR_FASTP { ext.args = '--quiet' publishDir = [ - path: { "${params.outdir}/fastqc_for_trim" }, + path: { "${params.outdir}/fastqc_for_fastp" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf index ce5244f1..61cce26f 100644 --- a/subworkflows/local/trim_workflow.nf +++ b/subworkflows/local/trim_workflow.nf @@ -1,4 +1,3 @@ -include { FASTQC as FASTQC_FOR_TRIM } from '../../modules/nf-core/fastqc/main' include { FASTP } from '../../modules/nf-core/fastp/main' include { FASTQC as FASTQC_FOR_FASTP } from '../../modules/nf-core/fastqc/main' From a0ea41320f579d7046839a57dff637ea6a2da2c6 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 22 Nov 2023 15:43:46 +0100 Subject: [PATCH 238/264] rename trimmed fastqc files --- assets/multiqc_config.yml | 2 +- conf/modules.config | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index b21e8548..d521c656 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -34,7 +34,7 @@ module_order: name: "FastQC (trimmed)" info: "This section of the report shows FastQC results after adapter trimming." path_filters: - - "*.zip" + - "*_trimmed*.zip" - arriba: name: "Arriba visualisation" info: "This section of the report shows Arriba visualisation after FusionInspector analysis." diff --git a/conf/modules.config b/conf/modules.config index ef3e69ab..dd98ea0e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -77,6 +77,7 @@ process { withName: FASTQC_FOR_FASTP { ext.args = '--quiet' + ext.prefix = { "${meta.id}_trimmed" } publishDir = [ path: { "${params.outdir}/fastqc_for_fastp" }, mode: params.publish_dir_mode, From 8ed7167a8c81718f1a205d18062cafc4f0275406 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 11:44:47 +0100 Subject: [PATCH 239/264] add csv info from fusionreport csv in vcf_collect to insure position is present and propagate exon nb and transcript id to all entries of gtf as some do not have the info --- bin/vcf_collect.py | 101 ++++++++++++++++++++++++++++++++++++++------- 1 file changed, 87 insertions(+), 14 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index e83204c9..2401d2e8 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -11,11 +11,15 @@ logger = logging.getLogger() -# vcf_collect(args.fusioninspector, args.fusionreport, args.fusioninspector_gtf, args.hgnc, args.sample, args.out) - def vcf_collect( - fusioninspector_in_file: str, fusionreport_in_file: str, gtf: str, hgnc: str, sample: str, out_file + fusioninspector_in_file: str, + fusionreport_in_file: str, + gtf: str, + fusionreport_csv: str, + hgnc: str, + sample: str, + out_file, ) -> None: """ Process FusionInspector and FusionReport data, @@ -24,10 +28,11 @@ def vcf_collect( Args: fusioninspector_in_file (str): Path to FusionInspector input file. - fusionreport_in_file (str): Path to FusionReport input file. + fusionreport_in_file (str): Path to Fusion-report input file. sample (str): Sample name for the header. hgnc (str): Path to HGNC file. gtf (str): Path to output GTF file from FusionInspector in TSV format. + fusionreport_csv (str): Path to Fusion-report CSV output file. out (str): Output VCF file path. Adapted from: https://github.com/J35P312/MegaFusion @@ -67,6 +72,19 @@ def vcf_collect( ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) ] + + all_df.replace("", np.nan, inplace=True) + all_df = all_df.drop_duplicates() + + all_df[["exon_number", "transcript_version"]] = all_df[["exon_number", "transcript_version"]].replace(0, np.nan) + # Fill non-empty values within each group for 'exon_number' and 'transcript_version' + all_df["exon_number"] = all_df.groupby("PosA")["exon_number"].transform( + lambda x: x.fillna(method="ffill").fillna(method="bfill") + ) + all_df["transcript_version"] = all_df.groupby("PosA")["transcript_version"].transform( + lambda x: x.fillna(method="ffill").fillna(method="bfill") + ) + all_df = all_df.rename(columns={"transcript_version": "Left_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Left_exon_number"}) all_df = all_df[ @@ -105,6 +123,18 @@ def vcf_collect( | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) ] + all_df[["PosA", "PosB"]] = all_df[["PosA", "PosB"]].replace(0, np.nan) + all_df = all_df.replace("", np.nan) + + all_df[["exon_number", "transcript_version"]] = all_df[["exon_number", "transcript_version"]].replace(0, np.nan) + # Fill non-empty values within each group for 'exon_number' and 'transcript_version' + all_df["exon_number"] = all_df.groupby("PosB")["exon_number"].transform( + lambda x: x.fillna(method="ffill").fillna(method="bfill") + ) + all_df["transcript_version"] = all_df.groupby("PosB")["transcript_version"].transform( + lambda x: x.fillna(method="ffill").fillna(method="bfill") + ) + all_df = all_df.rename(columns={"transcript_version": "Right_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Right_exon_number"}) @@ -138,6 +168,10 @@ def vcf_collect( "annots", ] ].drop_duplicates() + all_df = all_df.rename(columns={"FUSION": "Fusion"}) + all_df = all_df.set_index("Fusion") + + all_df = all_df.combine_first(read_fusionreport_csv(fusionreport_csv)) return write_vcf(column_manipulation(all_df), header_def(sample), out_file) @@ -309,10 +343,39 @@ def read_build_fusionreport(fusionreport_file: str) -> pd.DataFrame: ["FUSION"] ) -def read_fusionreport_csv(file: str) -> pd.DataFrame: - df = pd.read_csv(file, sep="\t") - +def read_fusionreport_csv(file: str) -> pd.DataFrame: + df = pd.read_csv(file) + df[["starfusion", "arriba", "fusioncatcher"]] = df[["starfusion", "arriba", "fusioncatcher"]].astype("str") + columns_to_iterate = ["starfusion", "arriba", "fusioncatcher"] + for index, row in df.iterrows(): + for column in columns_to_iterate: + cell_value = row[column] + + if "#" in cell_value: + df.at[index, column] = df.at[index, column].split(",")[0] + df.at[index, column] = df.at[index, column].replace("position: ", "") + df.at[index, "A"] = df.at[index, column].split("#")[0] + df.at[index, "B"] = df.at[index, column].split("#")[1] + df.at[index, "ChromosomeA"] = df.at[index, "A"].split(":")[0] + df.at[index, "PosA"] = df.at[index, "A"].split(":")[1] + if "+" in df.at[index, "A"] or "-" in df.at[index, "A"]: + df.at[index, "StrandA"] = df.at[index, "A"].split(":")[2] + else: + df.at[index, "StrandA"] = "" + + df.at[index, "ChromosomeB"] = df.at[index, "B"].split(":")[0] + df.at[index, "PosB"] = df.at[index, "B"].split(":")[1] + if "+" in df.at[index, "B"] or "-" in df.at[index, "B"]: + df.at[index, "StrandB"] = df.at[index, "B"].split(":")[2] + else: + df.at[index, "StrandB"] = "" + + break + df[["GeneA", "GeneB"]] = df["Fusion"].str.split("--", expand=True) + df = df.set_index("Fusion") + df.to_csv("tmp.csv") + return df[["GeneA", "GeneB", "ChromosomeA", "PosA", "StrandA", "ChromosomeB", "PosB", "StrandB"]] def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: @@ -340,13 +403,14 @@ def column_manipulation(df: pd.DataFrame) -> pd.DataFrame: df["Right_exon_number"] = df["Right_exon_number"].fillna(0).astype(int).astype(str) df["Left_transcript_version"] = df["Left_transcript_version"].fillna(0).astype(int).astype(str) df["Right_transcript_version"] = df["Right_transcript_version"].fillna(0).astype(int).astype(str) + df["PosA"] = df["PosA"].fillna(0).astype(int).astype(str) + df["PosB"] = df["PosB"].fillna(0).astype(int).astype(str) + df["PROT_FUSION_TYPE"] = df["PROT_FUSION_TYPE"].replace(".", "nan") + df["CDS_LEFT_ID"] = df["CDS_LEFT_ID"].replace(".", "nan") + df["CDS_RIGHT_ID"] = df["CDS_RIGHT_ID"].replace(".", "nan") for index, row in df.iterrows(): - if row["Strand1"] == "nan": - df.loc[index, "ALT"] = "nan" - elif not row["Strand1"] in ["+", "-"] or not row["Strand2"] in ["+", "-"]: - df.loc[index, "ALT"] = f'N[{df["ChromosomeB"]}:{row["PosB"]}[' - elif row["Strand1"] == "-" and row["Strand2"] == "-": + if row["Strand1"] == "-" and row["Strand2"] == "-": df.loc[index, "ALT"] = f'[{row["ChromosomeB"]}:{row["PosB"]}[N' elif row["Strand1"] == "+" and row["Strand2"] == "-": df.loc[index, "ALT"] = f'N]{row["ChromosomeB"]}:{row["PosB"]}]' @@ -411,7 +475,7 @@ def build_gtf_dataframe(file: str) -> pd.DataFrame: df = pd.read_csv(file, sep="\t") df[["fusion_dump", "Transcript_id"]] = df["transcript_id"].str.split("^", expand=True) df[["orig_chromosome", "orig_start", "orig_end", "orig_dir"]] = df["orig_coord_info"].str.split(",", expand=True) - return df[["Transcript_id", "transcript_version", "exon_number", "exon_id", "orig_start", "orig_end"]] + return df[["Transcript_id", "transcript_version", "exon_number", "orig_start", "orig_end"]] def main(argv=None): @@ -421,11 +485,20 @@ def main(argv=None): not args.fusioninspector.is_file() or not args.fusionreport.is_file() or not args.fusioninspector_gtf + or not args.fusionreport_csv or not args.hgnc ): logger.error(f"The given input file {args.fusioninspector} or {args.fusionreport} was not found!") sys.exit(2) - vcf_collect(args.fusioninspector, args.fusionreport, args.fusioninspector_gtf, args.hgnc, args.sample, args.out) + vcf_collect( + args.fusioninspector, + args.fusionreport, + args.fusioninspector_gtf, + args.fusionreport_csv, + args.hgnc, + args.sample, + args.out, + ) if __name__ == "__main__": From e91639db52e5700be5180f0eca85aebad169f39f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 11:48:20 +0100 Subject: [PATCH 240/264] add channel i/o for new input fusionreport csv --- modules/local/vcf_collect/main.nf | 4 ++-- subworkflows/local/fusioninspector_workflow.nf | 3 ++- workflows/rnafusion.nf | 1 + 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/local/vcf_collect/main.nf b/modules/local/vcf_collect/main.nf index 2af4a777..3ede7936 100644 --- a/modules/local/vcf_collect/main.nf +++ b/modules/local/vcf_collect/main.nf @@ -8,7 +8,7 @@ process VCF_COLLECT { 'quay.io/biocontainers/pandas:1.5.2' }" input: - tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report) + tuple val(meta), path(fusioninspector_tsv), path(fusioninspector_gtf_tsv), path(fusionreport_report), path(fusionreport_csv) tuple val(meta2), path(hgnc_ref) tuple val(meta3), path(hgnc_date) @@ -22,7 +22,7 @@ process VCF_COLLECT { script: def prefix = task.ext.prefix ?: "${meta.id}" """ - vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf + vcf_collect.py --fusioninspector $fusioninspector_tsv --fusionreport $fusionreport_report --fusioninspector_gtf $fusioninspector_gtf_tsv --fusionreport_csv $fusionreport_csv --hgnc $hgnc_ref --sample ${prefix} --out ${prefix}_fusion_data.vcf gzip ${prefix}_fusion_data.vcf cat <<-END_VERSIONS > versions.yml diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 32173e81..b2d7d791 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -10,6 +10,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { fusion_list fusion_list_filtered fusionreport_out + fusionreport_csv bam_sorted_indexed ch_gtf ch_arriba_ref_protein_domains @@ -45,7 +46,7 @@ workflow FUSIONINSPECTOR_WORKFLOW { AGAT_CONVERTSPGFF2TSV(FUSIONINSPECTOR.out.out_gtf) ch_versions = ch_versions.mix(AGAT_CONVERTSPGFF2TSV.out.versions) - fusion_data = FUSIONINSPECTOR.out.tsv_coding_effect.join(AGAT_CONVERTSPGFF2TSV.out.tsv).join(fusionreport_out) + fusion_data = FUSIONINSPECTOR.out.tsv_coding_effect.join(AGAT_CONVERTSPGFF2TSV.out.tsv).join(fusionreport_out).join(fusionreport_csv) VCF_COLLECT(fusion_data, ch_hgnc_ref, ch_hgnc_date) ch_versions = ch_versions.mix(VCF_COLLECT.out.versions) diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 6792eff8..5a587eeb 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -222,6 +222,7 @@ workflow RNAFUSION { FUSIONREPORT_WORKFLOW.out.fusion_list, FUSIONREPORT_WORKFLOW.out.fusion_list_filtered, FUSIONREPORT_WORKFLOW.out.report, + FUSIONREPORT_WORKFLOW.out.csv, STARFUSION_WORKFLOW.out.ch_bam_sorted_indexed, ch_chrgtf, ch_arriba_ref_protein_domains, From a568a9c7a7d526ac36ec296640117c42b5085ee9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 11:50:51 +0100 Subject: [PATCH 241/264] fusioninspector not sensititve --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 39135aa3..61535a7e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -94,7 +94,7 @@ process { withName: FUSIONINSPECTOR { ext.when = { !params.skip_vis } ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' } - ext.args2 = '--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect' + ext.args2 = '--annotate --examine_coding_effect' } withName: FUSIONREPORT { From 15e4a54e87f56cb029a81a41430ec1aa67fde399 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 12:55:57 +0100 Subject: [PATCH 242/264] fix channel io --- subworkflows/local/fusionreport_workflow.nf | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/fusionreport_workflow.nf b/subworkflows/local/fusionreport_workflow.nf index 92dc8f42..632ba2a3 100644 --- a/subworkflows/local/fusionreport_workflow.nf +++ b/subworkflows/local/fusionreport_workflow.nf @@ -12,6 +12,7 @@ workflow FUSIONREPORT_WORKFLOW { main: ch_versions = Channel.empty() ch_report = Channel.empty() + ch_csv = Channel.empty() if (!params.fusioninspector_only) { reads_fusions = reads @@ -24,6 +25,7 @@ workflow FUSIONREPORT_WORKFLOW { ch_fusion_list_filtered = FUSIONREPORT.out.fusion_list_filtered ch_versions = ch_versions.mix(FUSIONREPORT.out.versions) ch_report = FUSIONREPORT.out.report + ch_csv = FUSIONREPORT.out.csv } else { ch_fusion_list = reads.combine(Channel.value(file(params.fusioninspector_fusions, checkIfExists:true))) .map { meta, reads, fusions -> [ meta, fusions ] } @@ -35,6 +37,8 @@ workflow FUSIONREPORT_WORKFLOW { versions = ch_versions.ifEmpty(null) fusion_list = ch_fusion_list fusion_list_filtered = ch_fusion_list_filtered - report = ch_report.ifEmpty(null) + report = ch_report.ifEmpty(null) + csv = ch_csv.ifEmpty(null) + } From 716a852dc1466fdc91b87f09936131e8a7c3fc95 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 13:02:49 +0100 Subject: [PATCH 243/264] revert vcf --- bin/vcf_collect.py | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 5d359107..b5ff126d 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -63,24 +63,10 @@ def vcf_collect( all_df = df.merge(gtf_df, how="left", left_on="CDS_LEFT_ID", right_on="Transcript_id") all_df[["PosA", "orig_start", "orig_end"]] = all_df[["PosA", "orig_start", "orig_end"]].fillna(0).astype(int) - all_df["bla"] = ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) | ( - (all_df["orig_start"] == 0) & (all_df["orig_end"] == 0) - ) - all_df = all_df[ ((all_df["PosA"] >= all_df["orig_start"]) & (all_df["PosA"] <= all_df["orig_end"])) | ((all_df["orig_start"] == 0) & (all_df["orig_end"] == 0)) ] - - all_df.replace("", np.nan, inplace=True) - # Fill non-empty values within each group for 'exon_number' and 'transcript_version' - all_df["exon_number"] = all_df.groupby("PosA")["exon_number"].transform( - lambda x: x.fillna(method="ffill").fillna(method="bfill") - ) - all_df["transcript_version"] = all_df.groupby("PosA")["transcript_version"].transform( - lambda x: x.fillna(method="ffill").fillna(method="bfill") - ) - all_df = all_df.rename(columns={"transcript_version": "Left_transcript_version"}) all_df = all_df.rename(columns={"exon_number": "Left_exon_number"}) all_df = all_df[ From a76b16282e8d6a6bddde952396b9c45732dff412 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 13:03:36 +0100 Subject: [PATCH 244/264] revert fusioninspector filtering --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index dd98ea0e..90759b92 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -100,7 +100,7 @@ process { withName: FUSIONINSPECTOR { ext.when = { !params.skip_vis } ext.args = { params.fusioninspector_limitSjdbInsertNsj != 1000000 ? "--STAR_xtra_params \"--limitSjdbInsertNsj ${params.fusioninspector_limitSjdbInsertNsj}\"" : '' } - ext.args2 = '--annotate --examine_coding_effect' + ext.args2 = '--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect' } withName: FUSIONREPORT { From 04d57f07dc1f438f0c150413d316a08c17142ff1 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 14:02:06 +0100 Subject: [PATCH 245/264] Update assets/multiqc_config.yml Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- assets/multiqc_config.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d521c656..2b2a1e5e 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -35,8 +35,3 @@ module_order: info: "This section of the report shows FastQC results after adapter trimming." path_filters: - "*_trimmed*.zip" - - arriba: - name: "Arriba visualisation" - info: "This section of the report shows Arriba visualisation after FusionInspector analysis." - path_filters: - - "*.pdf" From 3fd02892631ebb4175780408e6793afbd9e65e34 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 14:02:41 +0100 Subject: [PATCH 246/264] Update assets/multiqc_config.yml Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- assets/multiqc_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 2b2a1e5e..5930000d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -24,12 +24,12 @@ run_modules: - arriba module_order: + - fastp - fastqc: name: "FastQC (raw)" info: "This section of the report shows FastQC results before adapter trimming." path_filters: - "*.zip" - - fastp - fastqc: name: "FastQC (trimmed)" info: "This section of the report shows FastQC results after adapter trimming." From 113dd9e01346ac2eb48f1365e332acab37f56702 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 14:05:11 +0100 Subject: [PATCH 247/264] udpate changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c40c613c..5116c32a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416) - Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420) +- Update modules, and make sure MultiQC displays the QC results properly [#440](https://github.com/nf-core/rnafusion/pull/440) ### Removed From 652cbd73098d76055615a3afa9cf11eb9d6c20ae Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 14:38:28 +0100 Subject: [PATCH 248/264] add conditions for collectinsertsize running --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index 39135aa3..b7b5445c 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -165,6 +165,7 @@ process { } withName: PICARD_COLLECTINSERTSIZEMETRICS { + ext.when = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all) } ext.prefix = { "${meta.id}_collectinsertsize"} publishDir = [ path: { "${params.outdir}/picard" }, From dead314a02148e295b1f826f128e04375a2ad7ec Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 14:39:55 +0100 Subject: [PATCH 249/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c40c613c..612e0ea1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416) - Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420) +- Add 'when' condition to run collectinsertsize [#444](https://github.com/nf-core/rnafusion/pull/444) ### Removed From 635bee670671fa130f4f0a6cd11ab9328b0d2b15 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 15:10:00 +0100 Subject: [PATCH 250/264] update fusionreport --- CHANGELOG.md | 1 + modules/local/fusionreport/detect/main.nf | 2 +- modules/local/fusionreport/download/main.nf | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 612e0ea1..1351fba3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430) - AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433) - Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) +- Update `fusion-report` to 2.1.8, removing FusionGDB database [#445](https://github.com/nf-core/rnafusion/pull/445) ### Fixed diff --git a/modules/local/fusionreport/detect/main.nf b/modules/local/fusionreport/detect/main.nf index 6060e0ae..8024d8f8 100644 --- a/modules/local/fusionreport/detect/main.nf +++ b/modules/local/fusionreport/detect/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p8" + container "docker.io/clinicalgenomics/fusion-report:2.1.8" input: diff --git a/modules/local/fusionreport/download/main.nf b/modules/local/fusionreport/download/main.nf index 220b51c9..ac288ade 100644 --- a/modules/local/fusionreport/download/main.nf +++ b/modules/local/fusionreport/download/main.nf @@ -3,7 +3,7 @@ process FUSIONREPORT_DOWNLOAD { label 'process_medium' conda "bioconda::star=2.7.9a" - container "docker.io/clinicalgenomics/fusion-report:2.1.5p8" + container "docker.io/clinicalgenomics/fusion-report:2.1.8" input: val(username) From 4a216e796eabd6cdad838b6869788f34fe223c0b Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 15:27:23 +0100 Subject: [PATCH 251/264] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c40c613c..a79e6013 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430) - AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433) - Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) +- Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443) ### Fixed From 459684900345f7745925b689789128aee89aaaf4 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Fri, 24 Nov 2023 15:39:49 +0100 Subject: [PATCH 252/264] update doc --- CHANGELOG.md | 1 + docs/output.md | 5 ++--- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 95813b7f..c9e18d9c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433) - Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) - Update `fusion-report` to 2.1.8, removing FusionGDB database [#445](https://github.com/nf-core/rnafusion/pull/445) +- Update documentation [#446](https://github.com/nf-core/rnafusion/pull/446) ### Fixed diff --git a/docs/output.md b/docs/output.md index 559e5fb2..dede2c87 100644 --- a/docs/output.md +++ b/docs/output.md @@ -222,9 +222,8 @@ The score is explained here: Date: Fri, 24 Nov 2023 15:41:15 +0100 Subject: [PATCH 253/264] update changelof --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 83ee977e..bfcfa21a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430) - AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433) - Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) -- Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443) +- Remove `--max_sensitivity --max_mate_dist 10000000` from fusioninspector. Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443) ### Fixed From df7a7b33583e2cebfa5218d3f19d6506926559e7 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 13:01:58 +0100 Subject: [PATCH 254/264] Update CHANGELOG.md Co-authored-by: Alexander Peltzer --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f6636747..2c0a4278 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.0.0dev - [date] +## v3.0.0 - [2023-11-28] ### Added From c4526a906a636ba7e38f9e9516d25ba2d8b27e9c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:12:38 +0100 Subject: [PATCH 255/264] Update tower.yml Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- tower.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tower.yml b/tower.yml index 66b54368..2edf5a7f 100644 --- a/tower.yml +++ b/tower.yml @@ -13,7 +13,7 @@ reports: display: "FusionInspector TSV report" "**/fusionreport/*/*_fusionreport_index.html": display: "Fusion-report HTML report" - "**/vcf_collect/*_fusion_data.vcf": + "**/vcf/*_fusion_data.vcf.gz": display: "Collected statistics on each fusion fed to FusionInspector in VCF format" "**/picard/*.MarkDuplicates.metrics.txt": display: "Picard: Metrics from CollectRnaMetrics" From cbf73a1093dfaa80467c3efe1d9f97cdf8f9d42f Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:15:30 +0100 Subject: [PATCH 256/264] bump version and remove igenomes param --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5930000d..6e00ca8c 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: nf-core-rnafusion-methods-description: diff --git a/nextflow.config b/nextflow.config index ebaafb30..7570a93b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -115,7 +115,7 @@ params { // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' + validationSchemaIgnoreParams = 'genomes' validationShowHiddenParams = false validate_params = true } @@ -290,7 +290,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.0.0dev' + version = '3.0.0' doi = '' } From 89075bb949dea394667da7e2646002eb60532dd0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:19:55 +0100 Subject: [PATCH 257/264] update modules --- modules.json | 8 +- modules/nf-core/star/align/main.nf | 4 +- modules/nf-core/star/align/tests/main.nf.test | 339 ++++++++ .../star/align/tests/main.nf.test.snap | 769 ++++++++++++++++++ .../star/align/tests/nextflow.arriba.config | 14 + .../nf-core/star/align/tests/nextflow.config | 14 + .../align/tests/nextflow.starfusion.config | 14 + modules/nf-core/star/align/tests/tags.yml | 2 + modules/nf-core/star/genomegenerate/main.nf | 4 +- .../star/genomegenerate/tests/main.nf.test | 38 + .../genomegenerate/tests/main.nf.test.snap | 16 + .../star/genomegenerate/tests/tags.yml | 2 + .../stringtie/merge/tests/main.nf.test | 82 ++ .../stringtie/merge/tests/main.nf.test.snap | 34 + .../nf-core/stringtie/merge/tests/tags.yml | 2 + .../stringtie/stringtie/tests/main.nf.test | 108 +++ .../stringtie/tests/main.nf.test.snap | 186 +++++ .../stringtie/stringtie/tests/tags.yml | 2 + nextflow_schema.json | 1 - 19 files changed, 1630 insertions(+), 9 deletions(-) create mode 100644 modules/nf-core/star/align/tests/main.nf.test create mode 100644 modules/nf-core/star/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/align/tests/nextflow.arriba.config create mode 100644 modules/nf-core/star/align/tests/nextflow.config create mode 100644 modules/nf-core/star/align/tests/nextflow.starfusion.config create mode 100644 modules/nf-core/star/align/tests/tags.yml create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test create mode 100644 modules/nf-core/star/genomegenerate/tests/main.nf.test.snap create mode 100644 modules/nf-core/star/genomegenerate/tests/tags.yml create mode 100644 modules/nf-core/stringtie/merge/tests/main.nf.test create mode 100644 modules/nf-core/stringtie/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/stringtie/merge/tests/tags.yml create mode 100644 modules/nf-core/stringtie/stringtie/tests/main.nf.test create mode 100644 modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap create mode 100644 modules/nf-core/stringtie/stringtie/tests/tags.yml diff --git a/modules.json b/modules.json index d13e5998..345e65b8 100644 --- a/modules.json +++ b/modules.json @@ -92,22 +92,22 @@ }, "star/align": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "9f6b233518f7d9ecdcf24b798b7e491db5424273", "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "0e98289b5bec6e3f8f588a8a9d05e8aacc1179a0", "installed_by": ["modules"] }, "stringtie/merge": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "b0dcb44b018d9b2bcb35b1abb7bcd34061bc5a6d", "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "b0dcb44b018d9b2bcb35b1abb7bcd34061bc5a6d", "installed_by": ["modules"] } } diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index fa645a6d..cc4f5af5 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -4,8 +4,8 @@ process STAR_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:019f262d90511939dce2dca4b7c868fc108f73db-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:019f262d90511939dce2dca4b7c868fc108f73db-0' }" input: tuple val(meta), path(reads, stageAs: "input*/*") diff --git a/modules/nf-core/star/align/tests/main.nf.test b/modules/nf-core/star/align/tests/main.nf.test new file mode 100644 index 00000000..4c878474 --- /dev/null +++ b/modules/nf-core/star/align/tests/main.nf.test @@ -0,0 +1,339 @@ +nextflow_process { + + name "Test Process STAR_ALIGN" + script "../main.nf" + process "STAR_ALIGN" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/align" + + test("homo_sapiens - single_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true) ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - single_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - single_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - single_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - single_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - single_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - single_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - single_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - single_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - single_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - single_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - single_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - single_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - single_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - single_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - single_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - single_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - log_out") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - junction") }, + { assert snapshot(process.out.log_progress).match("homo_sapiens - paired_end - log_progress") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - versions") } + ) + } + } + + test("homo_sapiens - paired_end - arriba") { + config "./nextflow.arriba.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - arriba - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - arriba - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - arriba - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - arriba - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - arriba - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - arriba - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - arriba - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - arriba - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - arriba - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - arriba - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - arriba - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - arriba - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - arriba - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - arriba - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - arriba - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - arriba - versions") } + ) + } + } + + test("homo_sapiens - paired_end - starfusion") { + config "./nextflow.starfusion.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - starfusion - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - starfusion - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - starfusion - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - starfusion - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - starfusion - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - starfusion - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - starfusion - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - starfusion - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - starfusion - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - starfusion - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - starfusion - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - starfusion - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - starfusion - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - starfusion - versions") } + ) + } + } + + test("homo_sapiens - paired_end - multiple") { + config "./nextflow.config" + + setup { + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + } + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.log_final[0][1]).name).match("homo_sapiens - paired_end - multiple - log_final") }, + { assert snapshot(file(process.out.log_out[0][1]).name).match("homo_sapiens - paired_end - multiple - log_out") }, + { assert snapshot(file(process.out.log_progress[0][1]).name).match("homo_sapiens - paired_end - multiple - log_progress") }, + { assert snapshot(process.out.bam).match("homo_sapiens - paired_end - multiple - bam") }, + { assert snapshot(process.out.bam_sorted).match("homo_sapiens - paired_end - multiple - bam_sorted") }, + { assert snapshot(process.out.bam_transcript).match("homo_sapiens - paired_end - multiple - bam_transcript") }, + { assert snapshot(process.out.bam_unsorted).match("homo_sapiens - paired_end - multiple - bam_unsorted") }, + { assert snapshot(process.out.bedgraph).match("homo_sapiens - paired_end - multiple - bedgraph") }, + { assert snapshot(process.out.fastq).match("homo_sapiens - paired_end - multiple - fastq") }, + { assert snapshot(process.out.junction).match("homo_sapiens - paired_end - multiple - junction") }, + { assert snapshot(process.out.read_per_gene_tab).match("homo_sapiens - paired_end - multiple - read_per_gene_tab") }, + { assert snapshot(process.out.sam).match("homo_sapiens - paired_end - multiple - sam") }, + { assert snapshot(process.out.spl_junc_tab).match("homo_sapiens - paired_end - multiple - spl_junc_tab") }, + { assert snapshot(process.out.tab).match("homo_sapiens - paired_end - multiple - tab") }, + { assert snapshot(process.out.wig).match("homo_sapiens - paired_end - multiple - wig") }, + { assert snapshot(process.out.versions).match("homo_sapiens - paired_end - multiple - versions") } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap new file mode 100644 index 00000000..59b735d4 --- /dev/null +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -0,0 +1,769 @@ +{ + "homo_sapiens - paired_end - multiple - bam_sorted": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" + ] + ] + ], + "timestamp": "2023-11-23T13:29:01.19639" + }, + "homo_sapiens - 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single_end - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.SJ.out.tab:md5,75a516ab950fb958f40b29996474949c" + ] + ] + ], + "timestamp": "2023-11-23T13:22:55.226143" + }, + "homo_sapiens - paired_end - starfusion - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,19c3faa1bfa9a0cc5e4c45f17065b53a" + ] + ] + ], + "timestamp": "2023-11-23T13:27:56.337072" + }, + "homo_sapiens - single_end - log_out": { + "content": [ + "test.Log.out" + ], + "timestamp": "2023-11-23T13:22:55.126286" + }, + "homo_sapiens - paired_end - log_final": { + "content": [ + "test.Log.final.out" + ], + "timestamp": "2023-11-23T13:23:33.253884" + }, + "homo_sapiens - single_end - log_final": { + "content": [ + "test.Log.final.out" + ], + "timestamp": "2023-11-23T13:22:55.11799" + }, + "homo_sapiens - paired_end - bam_transcript": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.287684" + }, + "homo_sapiens - paired_end - starfusion - log_progress": { + "content": [ + "test.Log.progress.out" + ], + "timestamp": "2023-11-23T13:27:55.971484" + }, + "homo_sapiens - paired_end - multiple - bam_transcript": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:29:01.264176" + }, + "homo_sapiens - paired_end - multiple - read_per_gene_tab": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:29:01.596406" + }, + "homo_sapiens - single_end - read_per_gene_tab": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:22:55.205936" + }, + "homo_sapiens - paired_end - junction": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.340653" + }, + "homo_sapiens - paired_end - spl_junc_tab": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.SJ.out.tab:md5,844af19ab0fc8cd9a3f75228445aca0d" + ] + ] + ], + "timestamp": "2023-11-23T13:23:33.398603" + }, + "homo_sapiens - paired_end - starfusion - sam": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:27:56.300637" + }, + "homo_sapiens - paired_end - arriba - bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.out.bam:md5,c1b1747f5873f2d17762725636e891d5" + ] + ] + ], + "timestamp": "2023-11-23T13:25:06.887604" + }, + "homo_sapiens - single_end - log_progress": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test.Log.progress.out:md5,b2bd061d6cbaaf3d6d3b1fed547f69b8" + ] + ] + ], + "timestamp": "2023-11-23T13:22:55.195544" + }, + "homo_sapiens - paired_end - starfusion - wig": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:27:56.422018" + }, + "homo_sapiens - paired_end - wig": { + "content": [ + [ + + ] + ], + "timestamp": "2023-11-23T13:23:33.429457" + }, + "homo_sapiens - paired_end - starfusion - log_out": { + "content": [ + "test.Log.out" + ], + "timestamp": "2023-11-23T13:27:55.93945" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config new file mode 100644 index 00000000..2324b9e5 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config new file mode 100644 index 00000000..c4ac5808 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config new file mode 100644 index 00000000..467b6497 --- /dev/null +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -0,0 +1,14 @@ +process { + + withName: STAR_GENOMEGENERATE { + ext.args = '--genomeSAindexNbases 9' + } + + withName: STAR_ALIGN { + ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outReadsUnmapped None --twopassMode Basic --outSAMstrandField intronMotif --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 8 --chimOutJunctionFormat 1 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --alignSJstitchMismatchNmax 5 -1 5 5 --chimMultimapScoreRange 3 --chimScoreJunctionNonGTAG -4 --chimMultimapNmax 20 --chimNonchimScoreDropMin 10 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --alignInsertionFlush Right --alignSplicedMateMapLminOverLmate 0 --alignSplicedMateMapLmin 30' + } + +} + +// Fix chown issue for the output star folder +docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/tags.yml b/modules/nf-core/star/align/tests/tags.yml new file mode 100644 index 00000000..8beace16 --- /dev/null +++ b/modules/nf-core/star/align/tests/tags.yml @@ -0,0 +1,2 @@ +star/align: + - modules/nf-core/star/align/** diff --git a/modules/nf-core/star/genomegenerate/main.nf b/modules/nf-core/star/genomegenerate/main.nf index 473e62a6..d2061844 100644 --- a/modules/nf-core/star/genomegenerate/main.nf +++ b/modules/nf-core/star/genomegenerate/main.nf @@ -4,8 +4,8 @@ process STAR_GENOMEGENERATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' : - 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:019f262d90511939dce2dca4b7c868fc108f73db-0' : + 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:019f262d90511939dce2dca4b7c868fc108f73db-0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test b/modules/nf-core/star/genomegenerate/tests/main.nf.test new file mode 100644 index 00000000..eed82926 --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test @@ -0,0 +1,38 @@ +nextflow_process { + + name "Test Process STAR_GENOMEGENERATE" + script "../main.nf" + process "STAR_GENOMEGENERATE" + tag "modules" + tag "modules_nfcore" + tag "star" + tag "star/genomegenerate" + + test("homo_sapiens") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.index[0][1]).name).match("index") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap new file mode 100644 index 00000000..bd4e0caa --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,9c11319b80fdedc90dadce4e0fb42ded" + ] + ], + "timestamp": "2023-11-23T11:18:14.835118" + }, + "index": { + "content": [ + "star" + ], + "timestamp": "2023-11-23T11:31:47.560528" + } +} \ No newline at end of file diff --git a/modules/nf-core/star/genomegenerate/tests/tags.yml b/modules/nf-core/star/genomegenerate/tests/tags.yml new file mode 100644 index 00000000..79f619bf --- /dev/null +++ b/modules/nf-core/star/genomegenerate/tests/tags.yml @@ -0,0 +1,2 @@ +star/genomegenerate: + - modules/nf-core/star/genomegenerate/** diff --git a/modules/nf-core/stringtie/merge/tests/main.nf.test b/modules/nf-core/stringtie/merge/tests/main.nf.test new file mode 100644 index 00000000..90368134 --- /dev/null +++ b/modules/nf-core/stringtie/merge/tests/main.nf.test @@ -0,0 +1,82 @@ +nextflow_process { + + name "Test Process STRINGTIE_MERGE" + script "../main.nf" + process "STRINGTIE_MERGE" + tag "modules" + tag "modules_nfcore" + tag "stringtie" + tag "stringtie/merge" + + test("homo_sapiens - forward strandedness") { + + setup { + run("STRINGTIE_STRINGTIE") { + script "../../stringtie/main.nf" + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + } + + when { + process { + """ + input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] } + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gtf).match("fs_gtf") }, + { assert snapshot(process.out.versions).match("fs_versions") } + ) + } + } + + test("homo_sapiens - reverse strandedness") { + + setup { + run("STRINGTIE_STRINGTIE") { + script "../../stringtie/main.nf" + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + } + + when { + process { + """ + input[0] = STRINGTIE_STRINGTIE.out.transcript_gtf.map { it -> it[1] } + input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.gtf).match("rs_gtf") }, + { assert snapshot(process.out.versions).match("rs_versions") } + ) + } + } +} diff --git a/modules/nf-core/stringtie/merge/tests/main.nf.test.snap b/modules/nf-core/stringtie/merge/tests/main.nf.test.snap new file mode 100644 index 00000000..3e4bc68f --- /dev/null +++ b/modules/nf-core/stringtie/merge/tests/main.nf.test.snap @@ -0,0 +1,34 @@ +{ + "rs_versions": { + "content": [ + [ + "versions.yml:md5,b73d45fdebf4c8c446bb01817db1665d" + ] + ], + "timestamp": "2023-11-23T14:14:39.697712988" + }, + "rs_gtf": { + "content": [ + [ + "stringtie.merged.gtf:md5,6da479298d73d5b3216d4e1576a2bdf4" + ] + ], + "timestamp": "2023-11-23T14:14:39.691894799" + }, + "fs_gtf": { + "content": [ + [ + "stringtie.merged.gtf:md5,d959eb2fab0db48ded7275e0a2e83c05" + ] + ], + "timestamp": "2023-11-23T14:14:20.872841278" + }, + "fs_versions": { + "content": [ + [ + "versions.yml:md5,b73d45fdebf4c8c446bb01817db1665d" + ] + ], + "timestamp": "2023-11-23T14:14:20.883140097" + } +} \ No newline at end of file diff --git a/modules/nf-core/stringtie/merge/tests/tags.yml b/modules/nf-core/stringtie/merge/tests/tags.yml new file mode 100644 index 00000000..58cef46b --- /dev/null +++ b/modules/nf-core/stringtie/merge/tests/tags.yml @@ -0,0 +1,2 @@ +stringtie/merge: + - modules/nf-core/stringtie/merge/** diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test b/modules/nf-core/stringtie/stringtie/tests/main.nf.test new file mode 100644 index 00000000..68786b74 --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test @@ -0,0 +1,108 @@ +nextflow_process { + + name "Test Process STRINGTIE_STRINGTIE" + script "../main.nf" + process "STRINGTIE_STRINGTIE" + tag "modules" + tag "modules_nfcore" + tag "stringtie" + tag "stringtie/stringtie" + + test("sarscov2 [bam] - forward strandedness") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("fs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_abundance") }, + { assert snapshot(process.out.versions).match("fs_versions") } + ) + } + } + + test("sarscov2 [bam] - forward strandedness + reference annotation") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'forward' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("fs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("fs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("fs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("fs_gtf_versions") } + ) + } + } + + test("sarscov2 [bam] - reverse strandedness") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("rs_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_abundance") }, + { assert snapshot(process.out.versions).match("rs_versions") } + ) + } + } + + test("sarscov2 [bam] - reverse strandedness + reference annotation") { + + when { + process { + """ + input[0] = [ + [ id:'test', strandedness:'reverse' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] + ] + input[1] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.transcript_gtf).match("rs_gtf_transcript_gtf") }, + { assert snapshot(process.out.abundance).match("rs_gtf_abundance") }, + { assert snapshot(process.out.ballgown).match("rs_gtf_ballgown") }, + { assert snapshot(process.out.versions).match("rs_gtf_versions") } + ) + } + } +} diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap new file mode 100644 index 00000000..bf751636 --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -0,0 +1,186 @@ +{ + "fs_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + ] + ] + ], + "timestamp": "2023-11-23T13:55:41.032044613" + }, + "fs_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + ] + ] + ], + "timestamp": "2023-11-23T13:55:41.017978904" + }, + "rs_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,d6f5c8cadb8458f1df0427cf790246e3" + ] + ] + ], + "timestamp": "2023-11-23T13:56:13.601112933" + }, + "fs_gtf_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:56:00.523797974" + }, + "fs_gtf_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + ] + ] + ], + "timestamp": "2023-11-23T13:56:00.475164879" + }, + "rs_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:56:13.623892691" + }, + "rs_gtf_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + ] + ] + ], + "timestamp": "2023-11-23T13:56:22.693599559" + }, + "fs_gtf_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + "test.gene.abundance.txt:md5,7d8bce7f2a922e367cedccae7267c22e" + ] + ] + ], + "timestamp": "2023-11-23T13:56:00.482135418" + }, + "rs_gtf_ballgown": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + [ + "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", + "e_data.ctab:md5,879b6696029d19c4737b562e9d149218", + "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", + "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", + "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" + ] + ] + ] + ], + "timestamp": "2023-11-23T13:56:22.715698347" + }, + "rs_transcript_gtf": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + ] + ] + ], + "timestamp": "2023-11-23T13:56:13.590054035" + }, + "rs_gtf_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:56:22.725513476" + }, + "fs_gtf_ballgown": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "forward" + }, + [ + "e2t.ctab:md5,e981c0038295ae54b63cedb1083f1540", + "e_data.ctab:md5,6b4cf69bc03f3f69890f972a0e8b7471", + "i2t.ctab:md5,8a117c8aa4334b4c2d4711932b006fb4", + "i_data.ctab:md5,be3abe09740603213f83d50dcf81427f", + "t_data.ctab:md5,3b66c065da73ae0dd41cc332eff6a818" + ] + ] + ] + ], + "timestamp": "2023-11-23T13:56:00.494299817" + }, + "fs_versions": { + "content": [ + [ + "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + ] + ], + "timestamp": "2023-11-23T13:55:41.049417582" + }, + "rs_gtf_abundance": { + "content": [ + [ + [ + { + "id": "test", + "strandedness": "reverse" + }, + "test.gene.abundance.txt:md5,7385b870b955dae2c2ab78a70cf05cce" + ] + ] + ], + "timestamp": "2023-11-23T13:56:22.701059059" + } +} diff --git a/modules/nf-core/stringtie/stringtie/tests/tags.yml b/modules/nf-core/stringtie/stringtie/tests/tags.yml new file mode 100644 index 00000000..da9b051c --- /dev/null +++ b/modules/nf-core/stringtie/stringtie/tests/tags.yml @@ -0,0 +1,2 @@ +stringtie/stringtie: + - modules/nf-core/stringtie/stringtie/** diff --git a/nextflow_schema.json b/nextflow_schema.json index 6dd54f7a..29ae6288 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -295,7 +295,6 @@ "description": "Path to FASTA genome file.", "fa_icon": "far fa-file-code" }, - "fai": { "type": "string", "format": "file-path", From 4ae96ff0f44e1d7fc1350f8a308eff6c4b09fa54 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:38:14 +0100 Subject: [PATCH 258/264] clarify changelog --- CHANGELOG.md | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2c0a4278..75d0ce76 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,36 +3,33 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v3.0.0 - [2023-11-28] +## v3.0.0 - [2023-11-27] ### Added -- Add picard CollectInserSizeMetrics to QC workflow [#408](https://github.com/nf-core/rnafusion/pull/408) -- Build CRAM index in the same directory as CRAM files for arriba and STAR-Fusion [#427](https://github.com/nf-core/rnafusion/pull/427) +- Add picard CollectInsertSizeMetrics to QC workflow [#408](https://github.com/nf-core/rnafusion/pull/408) +- Build CRAM index in the same directory as CRAM files for Arriba and STAR-Fusion [#427](https://github.com/nf-core/rnafusion/pull/427) ### Changed - Replace PICARD_MARKDUPLICATES with GATK4_MARKDUPLICATES [#409](https://github.com/nf-core/rnafusion/pull/409) - Removed `--fusioninspector_filter` and `--fusionreport_filter` in favor of `--tools_cutoff` (default = 1, no filters applied) [#389](https://github.com/nf-core/rnafusion/pull/389) -- Now publishing convert2bed output to convert2bed to keep the output file for mosdepth [#420](https://github.com/nf-core/rnafusion/pull/420) +- Now publishing convert2bed output to convert2bed to keep the output file [#420](https://github.com/nf-core/rnafusion/pull/420) - No more checks for existence of samplesheet, which made building references fail (building references uses a fake sample sheet if none is provided) [#420](https://github.com/nf-core/rnafusion/pull/420) -- `--extreme_sensitivity` used for fusioninspector to minimize fusioninspector filtering [#424](https://github.com/nf-core/rnafusion/pull/424) -- `--extreme_sensitivity` removed in favor of `--max_sensitivity --max_mate_dist 10000000 --annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) +- `--annotate --examine_coding_effect` to collect more data from fusioninspector [#426](https://github.com/nf-core/rnafusion/pull/426) +- Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443) - `Arriba` updated to 2.4.0 [#429](https://github.com/nf-core/rnafusion/pull/429) - Change megafusion into vcf_collect, taking into account e.g. the annotation and coding effects outputs from fusioninspector, HGNC ids, frame status... [#414](https://github.com/nf-core/rnafusion/pull/414) - CI tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#430](https://github.com/nf-core/rnafusion/pull/430) - AWS tests on `--all` instead of each tool separately, and include trimmed/not trimmed matrix tests [#433](https://github.com/nf-core/rnafusion/pull/433) -- Update `fusion-report` to 2.1.5p8 to fix download of references via proxy [#432](https://github.com/nf-core/rnafusion/pull/432) -- Remove `--max_sensitivity --max_mate_dist 10000000` from fusioninspector. Update vcf creation to get positions/chromosomes and strands even when fusions are filtered out by fusioninspector, using the csv output from fusion-report [#443](https://github.com/nf-core/rnafusion/pull/443) -- Update `fusion-report` to 2.1.8, removing FusionGDB database [#445](https://github.com/nf-core/rnafusion/pull/445) +- Update `fusion-report` to 2.1.8, updated COSMIC database to fix 404 error, fix download of references via proxy and removing FusionGDB database [#445](https://github.com/nf-core/rnafusion/pull/445) - Update documentation [#446](https://github.com/nf-core/rnafusion/pull/446) ### Fixed - Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416) -- Updated COSMIC database to fix 404 error while downloading fusionreport references [#420](https://github.com/nf-core/rnafusion/pull/420) - Update modules, and make sure MultiQC displays the QC results properly [#440](https://github.com/nf-core/rnafusion/pull/440) -- Add 'when' condition to run collectinsertsize [#444](https://github.com/nf-core/rnafusion/pull/444) +- Add 'when' condition to run CollectInsertSizeMetrics only when STAR-fusion bam files are available [#444](https://github.com/nf-core/rnafusion/pull/444) ### Removed From 3328c76087df70afbc0edf5eea568286e00ba9ff Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:51:58 +0100 Subject: [PATCH 259/264] update version to 4.0.0 --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 6e00ca8c..5930000d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: nf-core-rnafusion-methods-description: diff --git a/nextflow.config b/nextflow.config index 7570a93b..34f47361 100644 --- a/nextflow.config +++ b/nextflow.config @@ -290,7 +290,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '3.0.0' + version = '4.0.0dev' doi = '' } From 279daf42c6f84f26e067ff0f466511fbc4a33ecf Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 27 Nov 2023 16:53:03 +0100 Subject: [PATCH 260/264] prepare changelog for 4.0.0 --- CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 75d0ce76..08b1132f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v4.0.0 - [date] + +### Added + +### Changed + +### Fixed + +### Removed + ## v3.0.0 - [2023-11-27] ### Added From bb271bbf508a7b6a4998e978c6a4cd659ccfb64c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 12:03:09 +0100 Subject: [PATCH 261/264] fix versions --- modules/local/fusioncatcher/detect/main.nf | 4 ++-- subworkflows/local/arriba_workflow.nf | 2 +- subworkflows/local/fusioncatcher_workflow.nf | 3 ++- .../local/fusioninspector_workflow.nf | 2 +- subworkflows/local/fusionreport_workflow.nf | 2 +- subworkflows/local/qc_workflow.nf | 2 +- subworkflows/local/starfusion_workflow.nf | 2 +- subworkflows/local/stringtie_workflow.nf | 4 +++- subworkflows/local/trim_workflow.nf | 2 +- workflows/rnafusion.nf | 20 +++++++++---------- 10 files changed, 23 insertions(+), 20 deletions(-) diff --git a/modules/local/fusioncatcher/detect/main.nf b/modules/local/fusioncatcher/detect/main.nf index fa072bf4..2977d668 100644 --- a/modules/local/fusioncatcher/detect/main.nf +++ b/modules/local/fusioncatcher/detect/main.nf @@ -39,7 +39,7 @@ process FUSIONCATCHER { cat <<-END_VERSIONS > versions.yml "${task.process}": - fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1)| sed 's/fusioncatcher.py //') + fusioncatcher: \$(echo \$(fusioncatcher.py --version 2>&1)| sed 's/fusioncatcher.py //') END_VERSIONS """ @@ -52,7 +52,7 @@ process FUSIONCATCHER { touch ${prefix}.fusioncatcher.log cat <<-END_VERSIONS > versions.yml "${task.process}": - fusioncatcher: \$(echo \$(fusioncatcher --version 2>&1)| sed 's/fusioncatcher.py //') + fusioncatcher: \$(echo \$(fusioncatcher.py --version 2>&1)| sed 's/fusioncatcher.py //') END_VERSIONS """ } diff --git a/subworkflows/local/arriba_workflow.nf b/subworkflows/local/arriba_workflow.nf index 3aa9c090..f59018dc 100644 --- a/subworkflows/local/arriba_workflow.nf +++ b/subworkflows/local/arriba_workflow.nf @@ -59,6 +59,6 @@ workflow ARRIBA_WORKFLOW { emit: fusions = ch_arriba_fusions fusions_fail = ch_arriba_fusion_fail - versions = ch_versions.ifEmpty(null) + versions = ch_versions } diff --git a/subworkflows/local/fusioncatcher_workflow.nf b/subworkflows/local/fusioncatcher_workflow.nf index a9058dc6..ebb09e60 100644 --- a/subworkflows/local/fusioncatcher_workflow.nf +++ b/subworkflows/local/fusioncatcher_workflow.nf @@ -19,6 +19,7 @@ workflow FUSIONCATCHER_WORKFLOW { params.fusioncatcher_ref ) ch_fusioncatcher_fusions = FUSIONCATCHER.out.fusions + ch_versions = ch_versions.mix(FUSIONCATCHER.out.versions) } } else { @@ -28,6 +29,6 @@ workflow FUSIONCATCHER_WORKFLOW { emit: fusions = ch_fusioncatcher_fusions - versions = ch_versions.ifEmpty(null) + versions = ch_versions } diff --git a/subworkflows/local/fusioninspector_workflow.nf b/subworkflows/local/fusioninspector_workflow.nf index 48fcc19f..7a31d7cd 100644 --- a/subworkflows/local/fusioninspector_workflow.nf +++ b/subworkflows/local/fusioninspector_workflow.nf @@ -60,6 +60,6 @@ workflow FUSIONINSPECTOR_WORKFLOW { emit: ch_arriba_visualisation - versions = ch_versions.ifEmpty(null) + versions = ch_versions } diff --git a/subworkflows/local/fusionreport_workflow.nf b/subworkflows/local/fusionreport_workflow.nf index 632ba2a3..09ec9965 100644 --- a/subworkflows/local/fusionreport_workflow.nf +++ b/subworkflows/local/fusionreport_workflow.nf @@ -34,7 +34,7 @@ workflow FUSIONREPORT_WORKFLOW { } emit: - versions = ch_versions.ifEmpty(null) + versions = ch_versions fusion_list = ch_fusion_list fusion_list_filtered = ch_fusion_list_filtered report = ch_report.ifEmpty(null) diff --git a/subworkflows/local/qc_workflow.nf b/subworkflows/local/qc_workflow.nf index 576701e5..6b53358a 100644 --- a/subworkflows/local/qc_workflow.nf +++ b/subworkflows/local/qc_workflow.nf @@ -33,7 +33,7 @@ workflow QC_WORKFLOW { emit: - versions = ch_versions.ifEmpty(null) + versions = ch_versions rnaseq_metrics = ch_rnaseq_metrics duplicate_metrics = ch_duplicate_metrics insertsize_metrics = ch_insertsize_metrics diff --git a/subworkflows/local/starfusion_workflow.nf b/subworkflows/local/starfusion_workflow.nf index 38264c01..ec7a832c 100644 --- a/subworkflows/local/starfusion_workflow.nf +++ b/subworkflows/local/starfusion_workflow.nf @@ -60,7 +60,7 @@ workflow STARFUSION_WORKFLOW { star_gene_count = ch_star_gene_count ch_bam_sorted = ch_align.ifEmpty([[],[]]) ch_bam_sorted_indexed = bam_sorted_indexed.ifEmpty([[],[],[]]) - versions = ch_versions.ifEmpty(null) + versions = ch_versions } diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf index 93a50e0c..60bd4f38 100644 --- a/subworkflows/local/stringtie_workflow.nf +++ b/subworkflows/local/stringtie_workflow.nf @@ -20,6 +20,8 @@ workflow STRINGTIE_WORKFLOW { .transcript_gtf .map { it -> it[1] } .set { stringtie_gtf } + ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions) + STRINGTIE_MERGE (stringtie_gtf, ch_chrgtf.map { meta, gtf -> [ gtf ]}) ch_versions = ch_versions.mix(STRINGTIE_MERGE.out.versions) @@ -28,7 +30,7 @@ workflow STRINGTIE_WORKFLOW { emit: stringtie_gtf = ch_stringtie_gtf.ifEmpty(null) - versions = ch_versions.ifEmpty(null) + versions = ch_versions } diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf index 61cce26f..ea21134d 100644 --- a/subworkflows/local/trim_workflow.nf +++ b/subworkflows/local/trim_workflow.nf @@ -37,6 +37,6 @@ workflow TRIM_WORKFLOW { ch_fastp_html ch_fastp_json ch_fastqc_trimmed - versions = ch_versions.ifEmpty(null) + versions = ch_versions } diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 8319b49e..992f72fc 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -149,7 +149,7 @@ workflow RNAFUSION { .reads .mix(ch_fastq.single) .set { ch_cat_fastq } - ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions) // @@ -158,14 +158,14 @@ workflow RNAFUSION { FASTQC ( ch_cat_fastq ) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + ch_versions = ch_versions.mix(FASTQC.out.versions) TRIM_WORKFLOW ( ch_cat_fastq ) ch_reads_fusioncatcher = TRIM_WORKFLOW.out.ch_reads_fusioncatcher ch_reads_all = TRIM_WORKFLOW.out.ch_reads_all - + ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions) // Run STAR alignment and Arriba ARRIBA_WORKFLOW ( @@ -177,7 +177,7 @@ workflow RNAFUSION { ch_arriba_ref_known_fusions, ch_arriba_ref_protein_domains ) - ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(ARRIBA_WORKFLOW.out.versions) //Run STAR fusion @@ -187,14 +187,14 @@ workflow RNAFUSION { ch_starindex_ref, ch_fasta ) - ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(STARFUSION_WORKFLOW.out.versions) //Run fusioncatcher FUSIONCATCHER_WORKFLOW ( ch_reads_fusioncatcher ) - ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(FUSIONCATCHER_WORKFLOW.out.versions) //Run stringtie @@ -202,7 +202,7 @@ workflow RNAFUSION { STARFUSION_WORKFLOW.out.ch_bam_sorted, ch_chrgtf ) - ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(STRINGTIE_WORKFLOW.out.versions) //Run fusion-report @@ -213,7 +213,7 @@ workflow RNAFUSION { STARFUSION_WORKFLOW.out.fusions, FUSIONCATCHER_WORKFLOW.out.fusions ) - ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(FUSIONREPORT_WORKFLOW.out.versions) //Run fusionInpector @@ -230,7 +230,7 @@ workflow RNAFUSION { ch_hgnc_ref, ch_hgnc_date ) - ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(FUSIONINSPECTOR_WORKFLOW.out.versions) //QC @@ -243,7 +243,7 @@ workflow RNAFUSION { ch_fai, ch_rrna_interval ) - ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions.first().ifEmpty(null)) + ch_versions = ch_versions.mix(QC_WORKFLOW.out.versions) CUSTOM_DUMPSOFTWAREVERSIONS ( ch_versions.unique().collectFile(name: 'collated_versions.yml') From d264cead3a30c347fafbeeb2ade9dc339b9aa2c2 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 14:16:36 +0100 Subject: [PATCH 262/264] update changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08b1132f..e68ff0df 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v4.0.0 - [date] +## v3.0.1 - [2023-11-29] ### Added @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Fixed +- software-version.yml and in general version track-keeping was incomplete [#451](https://github.com/nf-core/rnafusion/pull/451) + ### Removed ## v3.0.0 - [2023-11-27] From 226b24a3db3eddc33e8a55fd481539a222b034f0 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 14:22:00 +0100 Subject: [PATCH 263/264] update version to 3.0.1 --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 5930000d..dd83ce70 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/rnafusion + This report has been generated by the nf-core/rnafusion analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: nf-core-rnafusion-methods-description: diff --git a/nextflow.config b/nextflow.config index 34f47361..3a54be0c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -290,7 +290,7 @@ manifest { description = """Nextflow rnafusion analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '4.0.0dev' + version = '3.0.1' doi = '' } From 35cb3feb7fbf8afe3511e3c28ef2618b9e96fd58 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Wed, 29 Nov 2023 14:28:54 +0100 Subject: [PATCH 264/264] - --- CHANGELOG.md | 2 ++ bin/vcf_collect.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08b1132f..70b6b9eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- python3 explicit in vcf_collect [#452](https://github.com/nf-core/rnafusion/pull/452) + ### Fixed ### Removed diff --git a/bin/vcf_collect.py b/bin/vcf_collect.py index 2401d2e8..a8ab85f4 100755 --- a/bin/vcf_collect.py +++ b/bin/vcf_collect.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python3 import argparse import logging