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update to version 2.0.0
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avantonder committed Nov 6, 2024
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13 changes: 13 additions & 0 deletions docs/output.md
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Expand Up @@ -17,6 +17,7 @@ and processes data using the following steps:
- [`Assign taxonomy to reads`](#assign-taxonomy-to-reads)
- [`Re-estimate taxonomy`](#re-estimate-taxonomy)
- [`Extract reads`](#extract-reads)
- [`Visualize taxonomy`](#visualize-taxonomy)
- [`Species composition`](#calculate-species-composition)
- [`Sequencing statistics`](#sequencing-statistics)
- [`MultiQC`](#multiqc)
Expand Down Expand Up @@ -113,6 +114,18 @@ and processes data using the following steps:

[KrakenTools](https://github.com/jenniferlu717/KrakenTools) is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results.

### Visualize taxonomy

<details markdown="1">
<summary>Output files</summary>

- `krona/`
- `*.html`: HTML files containing taxonomy visualizations

</details>

[Krona](https://pubmed.ncbi.nlm.nih.gov/21961884/) creates interactive metagenomic visualizations in a Web browser.

### Calculate species composition

<details markdown="1">
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104 changes: 58 additions & 46 deletions docs/parameters.md
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Expand Up @@ -8,46 +8,19 @@ Define where the pipeline should find input data and save output data.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>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. </small></details>| `string` | | | |
| `kraken2db` | Path to Kraken 2 database | `string` | None | | |
| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | | |
| `email` | Email address for completion summary. <details><summary>Help</summary><small>Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the
workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.</small></details>| `string` | | | |
| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>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.</small></details>| `string` | | True | |
| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | True | |
| `email` | Email address for completion summary. <details><summary>Help</summary><small>Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.</small></details>| `string` | | | |
| `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` | | | |

## Quality Control options



| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `skip_fastp` | Skip the fastp trimming step. | `boolean` | | | |
| `skip_fastqc` | Skip the fastQC step. | `boolean` | | | |
| `save_trimmed_fail` | Save failed trimmed reads. | `boolean` | | | |
| `skip_multiqc` | Skip MultiQC. | `boolean` | | | |
| `adapter_file` | Path to file containing adapters in FASTA format. | `string` | '${baseDir}/assets/adapters.fas' | | |
| `skip_kraken2` | Skip Kraken 2 and Bracken. | `boolean` | | | |
| `genome_size` | Specify a genome size to be used by fastq-scan to calculate coverage | `integer` | | | |

## Extract reads options



| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `kraken_extract` | Extract reads from fastq files based on taxon id | `boolean` | | | |
| `tax_id` | If --kraken_extract is used, --tax_is specifies the taxon id to be used to extract reads | `string` | | | |

## Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `custom_config_version` | Git commit id for Institutional configs. | `string` | master | | True |
| `custom_config_base` | Base directory for Institutional configs. <details><summary>Help</summary><small>If you're running offline, Nextflow will not be able to fetch the institutional config files
from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this
parameter.</small></details>| `string` | https://raw.githubusercontent.com/nf-core/configs/master | | True |
| `custom_config_base` | Base directory for Institutional configs. <details><summary>Help</summary><small>If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.</small></details>| `string` | https://raw.githubusercontent.com/nf-core/configs/master | | True |
| `config_profile_name` | Institutional config name. | `string` | | | True |
| `config_profile_description` | Institutional config description. | `string` | | | True |
| `config_profile_contact` | Institutional config contact information. | `string` | | | True |
Expand All @@ -59,12 +32,9 @@ Set the top limit for requested resources for any single job.

| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `max_cpus` | Maximum number of CPUs that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the CPU requirement for each process. Should be an
integer e.g. `--max_cpus 1`</small></details>| `integer` | 16 | | True |
| `max_memory` | Maximum amount of memory that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the memory requirement for each process. Should
be a string in the format integer-unit e.g. `--max_memory '8.GB'`</small></details>| `string` | 128.GB | | True |
| `max_time` | Maximum amount of time that can be requested for any single job. <details><summary>Help</summary><small>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'`</small></details>| `string` | 240.h | | True |
| `max_cpus` | Maximum number of CPUs that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`</small></details>| `integer` | 16 | | True |
| `max_memory` | Maximum amount of memory that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`</small></details>| `string` | 128.GB | | True |
| `max_time` | Maximum amount of time that can be requested for any single job. <details><summary>Help</summary><small>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'`</small></details>| `string` | 240.h | | True |

## Generic options

Expand All @@ -73,17 +43,59 @@ Less common options for the pipeline, typically set in a config file.
| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `help` | Display help text. | `boolean` | | | True |
| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>The Nextflow `publishDir` option specifies which intermediate files should be
saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for
details.</small></details>| `string` | copy | | True |
| `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send a summary email to when the pipeline is completed -
ONLY sent if the pipeline does not exit successfully.</small></details>| `string` | | | True |
| `version` | Display version and exit. | `boolean` | | | True |
| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.</small></details>| `string` | copy | | True |
| `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.</small></details>| `string` | | | True |
| `plaintext_email` | Send plain-text email instead of HTML. | `boolean` | | | True |
| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB | | True |
| `monochrome_logs` | Do not use coloured log outputs. | `boolean` | | | True |
| `hook_url` | Incoming hook URL for messaging service <details><summary>Help</summary><small>Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.</small></details>| `string` | | | True |
| `multiqc_config` | Custom config file to supply to MultiQC. | `string` | | | True |
| `tracedir` | Directory to keep pipeline Nextflow logs and reports. | `string` | ${params.outdir}/pipeline_info | | True |
| `multiqc_logo` | Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | `string` | | | True |
| `multiqc_methods_description` | Custom MultiQC yaml file containing HTML including a methods description. | `string` | | | |
| `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True | | True |
| `show_hidden_params` | Show all params when using `--help` <details><summary>Help</summary><small>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.</small></details>| `boolean` | | | True |
| `enable_conda` | Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter. | `boolean` | | | True |
| `validationShowHiddenParams` | Show all params when using `--help` <details><summary>Help</summary><small>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.</small></details>| `boolean` | | | True |
| `validationFailUnrecognisedParams` | Validation of parameters fails when an unrecognised parameter is found. <details><summary>Help</summary><small>By default, when an unrecognised parameter is found, it returns a warinig.</small></details>| `boolean` | | | True |
| `validationLenientMode` | Validation of parameters in lenient more. <details><summary>Help</summary><small>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).</small></details>| `boolean` | | | True |
| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/nf-core/test-datasets/ | | |

## FastQC/fastp options



| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `skip_fastqc` | Skip the fastQC step. | `boolean` | | | |
| `skip_fastp` | Skip the fastp trimming step. | `boolean` | | | |
| `adapter_fasta` | File in FASTA format containing possible adapters to remove. Accepted formats: *.{fasta,fna,fas,fa} | `string` | None | | |
| `save_trimmed_fail` | Specify `true` to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz | `boolean` | | | |
| `save_merged` | Specify true to save all merged reads to the a file ending in *.merged.fastq.gz | `boolean` | | | |
| `extra_fastp_args` | Extra arguments for fastp. For example, `--trim_front1 15 --trim_front2 15 --trim_tail1 5 --trim_tail2 5{:bash}` | `string` | None | | |

## fastq-scan options



| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `genome_size` | Specify a genome size to be used by fastq-scan to calculate coverage | `integer` | 2000000 | | |

## Kraken 2 options



| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `skip_kraken2` | Skip Kraken 2 and Bracken. | `boolean` | | | |
| `kraken2db` | Path to Kraken 2 database | `string` | None | | |
| `save_output_fastqs` | Turn on saving of Kraken2-aligned reads | `boolean` | | | |
| `save_reads_assignment` | Turn on saving of Kraken2 per-read taxonomic assignment file | `boolean` | True | | |
| `kraken_extract` | Extract reads from fastq files based on taxon id | `boolean` | | | |

## Krona options



| Parameter | Description | Type | Default | Required | Hidden |
|-----------|-----------|-----------|-----------|-----------|-----------|
| `kronadb` | Path to Krona taxonomy file | `string` | None | | |
9 changes: 9 additions & 0 deletions docs/usage.md
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Expand Up @@ -52,6 +52,14 @@ The pipeline can be provided with a path to a Kraken 2 database which is used, a

The Kraken 2 and Bracken steps can by skipped by specifying the `--skip_kraken2` parameter.

## Krona taxonomy file

The pipeline can be provided with a path to a Krona taxonomy file which creates HTML visualizations of the Bracken results. Use the `--kronadb` parameter to specify the location of the Krona taxonomy file:

```console
--kronadb '[path to Krona taxonomy file]'
```

## Genome size

The pipeline can be provided with a genome size which will be used by fastq-scan to calculate an approximate read coverage. Use the `--genome size` parameter to specify the genome size of the species being analysed:
Expand All @@ -69,6 +77,7 @@ nextflow run avantonder/bacQC \
--input samplesheet.csv \
-profile singularity \
--kraken2db path/to/kraken2/dir \
--kronadb path/to/kronataxonomy \
--genome_size <ESTIMATED GENOME SIZE> \
--outdir <OUTDIR> \
-resume
Expand Down

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