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Add sequali#134

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pontushojer wants to merge 239 commits intonf-core:devfrom
pontushojer:add-sequali
Open

Add sequali#134
pontushojer wants to merge 239 commits intonf-core:devfrom
pontushojer:add-sequali

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@pontushojer pontushojer commented Oct 23, 2025

Relates to #33

I have been using sequali with PacBio data and found it quite useful. I think its a great fit for seqinspector as it is intended for use with both short and long reads.

PR checklist

  • 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
  • If necessary, also make a PR on the nf-core/seqinspector branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

mahesh-panchal and others added 30 commits March 19, 2024 10:09
@mahesh-panchal
Update assets/schema_input.json
56e01a0
@alneberg @Aratz
grop instead of project in a single place
6c94332 
Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
@alneberg @mahesh-panchal
Updated test profile input
4779844
@alneberg @KarNair
Update assets/schema_input.json
28e0137 
Co-authored-by: Karthik Nair <35717861+KarNair@users.noreply.github.com>
@alneberg
Merge pull request nf-core#2 from mahesh-panchal/input_workflow
d169eef 
Input workflow
@Aratz
Generate reports per lane, group and rundir
a31040e
@Aratz
Improve formatting
0da5870
@Aratz
Improve output sorting
d233d8f
@Aratz
Use group instead of project
307e43c
@Aratz
Fix output channel
627cf94
@Aratz
Fix linting
c9ba028
@Aratz
Give credits back to NGI
2cfc91d
@Aratz
Fix file names
fbfb02d
@Aratz
Set up tests
8a19929
@kedhammar
point test conf upstream
eba628e
@kedhammar
project -> group
23f69d1
@kedhammar
project -> group
1ebf3f1
@kedhammar
make lane non-compulsory
b0bf471
@kedhammar
remove unused file
9e0eca3
@kedhammar
revamp nf-test, run once for each sequencing platform
98e60bf
@Aratz
Update modules and subworkflows
d95c660
@Aratz
Fix multiqc extra files
e0527cc 
Issue with the previous implementation was that sometimes
MULTIQC_PER_LANE would execute before the extra files were collected
into `ch_multiqc_extra_files`, causing `null` to be added to the list of
files passed to multiqc.
@MatthiasZepper
Merge branch 'dev' into nf-core-template-merge-2.14.1
ba72067
@Aratz
Add test snapshots
42159a1
@Aratz
Remove unused module configuration
ef61f9f
@Aratz
Update usage docs and restore example samplesheet
51b01e9
@Aratz
Update output docs
7c7f31f
@Aratz
Update changelog
1c4f6e0
@Aratz
Update samplesheet in readme file
211bfaf
@Aratz
Merge pull request nf-core#15 from nf-core/nf-core-template-merge-2.14.1
e93baf9 
Important! Template update for nf-core/tools v2.14.1
KarNair and others added 24 commits March 25, 2025 16:37
@KarNair
Merge pull request nf-core#103 from KarNair/dev
ae2d549 
Configure full-tests
@nkongenelly @Aratz
Put SeqFU-stats section reports together
4d8c75b 
Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>
Co-authored-by: Karthik Nair <karthik.nair@medsci.uu.se>"
@Aratz
Merge remote-tracking branch 'origin/dev' into multiple-seqfu-reports
d930935
@Aratz @nkongenelly @kedhammar
Fix tests
df1a244 
Co-authored-by: nelnk861 <nelly.nkonge@uu.se>
Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
@mahesh-panchal
Update schema to accept tar file or directory
0db3b72
@Aratz
Update changelog
70e66b8
@mahesh-panchal
Update CHANGELOG.md
04d8375
@Aratz
Lint changelog
bd65741
@mahesh-panchal
Merge pull request nf-core#110 from mahesh-panchal/add_rundir
bab7854 
Update rundir to accept either tar file or directory
@Aratz
Merge pull request nf-core#107 from nkongenelly/multiple-seqfu-reports
02005f8 
Put SeqFU-stats section reports together
@kedhammar
updates to fit incoming template conventions
f9446cd
@nkongenelly
Making fastq_screen_references value to use baseDir
90fb609
@kedhammar
ignore lint for missing ci.yml
250aace
@nkongenelly
Merge pull request nf-core#112 from nkongenelly/fastq_screen_referenc…
53940ea 
…es-baseDir-fix

Making fastq_screen_references value to use parentDir
@Aratz
Update MultiQC to 1.28
ef4c3a6 
Fixes nf-core#102
@Aratz
Update changelog
432f769
@Aratz
Lint changelog
71cd6de
@Aratz
Update snapshots
f28a1e1
@Aratz
Merge pull request nf-core#116 from Aratz/dev
0058879 
Update MultiQC to 1.28
@maxulysse
Merge branch 'dev' into ci-nf-test
cf5f9eb
@kedhammar
bump changelog
fda6189
@kedhammar
Merge pull request nf-core#114 from kedhammar/ci-nf-test
da768fb 
Update nf-test configuration and CI
@pontushojer
add sequali
35dcc5a
@pontushojer
update citations
d642856
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nf-core-bot commented Oct 23, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Oct 23, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2adc698

+| ✅ 189 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  16 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">\n <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_logo_light.png">\n \n

    \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/seqinspector is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/seqinspector \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> 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.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/seqinspector was originally written by Adrien Coulier.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #seqinspector channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/seqinspector for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-10-23 13:02:59

@FranBonath FranBonath added this to the 1.1.0 milestone Nov 6, 2025
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