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Adding Picard tools for QC metrics #128

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@agrima2010 agrima2010 commented Oct 1, 2025 •
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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).

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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 1, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e4948a0

+| ✅ 195 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  15 tests had warnings |!

❗ 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 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 \n\n1. Subsample reads (Seqtk)\n2. Read QC (FastQC)\n3. 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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2,rundir,tags\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,200624_A00834_0183_BHMTFYDRXX,lane1:project5:group2\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\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 the Swedish @NationalGenomicsInfrastructure.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- @mahesh-panchal\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 2025-10-28 12:37:45

@agrima2010 agrima2010 changed the title Picard tools dev Adding Picard tools for QC metrics Oct 2, 2025
@agrima2010 agrima2010 requested a review from FranBonath October 7, 2025 09:22
maxulysse
maxulysse reviewed Oct 7, 2025
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conf/test.config Outdated
Comment on lines 34 to 37
withLabel: 'process_high' {
cpus = 4
memory = '15.GB'
}
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nitpick(non-blocking)
You shouldn't need that

maxulysse
maxulysse reviewed Oct 7, 2025
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maxulysse
maxulysse reviewed Oct 7, 2025
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@agrima2010 agrima2010 requested a review from ramprasadn October 15, 2025 11:35
ramprasadn
ramprasadn reviewed Oct 27, 2025
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conf/modules.config
withName: 'SAMTOOLS_INDEX' {
ext.args = ''
publishDir = [
path: { "${params.outdir}/samtools_index" },
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I suggest publishing these files in the same folder as your bam/cram files.

Agrima Bhatt and others added 11 commits October 27, 2025 13:51
ss updated
5db6843
@agrima2010 @ramprasadn
Update conf/modules.config
08b7aea 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update conf/modules.config
44c75f6 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update conf/modules.config
da32a43 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update workflows/seqinspector.nf
10ebebf 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update workflows/seqinspector.nf
e6fa02f 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update workflows/seqinspector.nf
89376b5 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update workflows/seqinspector.nf
403752d 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
@agrima2010 @ramprasadn
Update workflows/seqinspector.nf
37d553f 
Co-authored-by: Ramprasad Neethiraj <[email protected]>
updated ss
6c1d138
ss updated
e4948a0
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