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Pipeline description in README #111

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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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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @Patricie34,

It looks like this pull-request is has been made against the Patricie34/seqinspector master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the Patricie34/seqinspector dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@Patricie34 Patricie34 changed the title Piepeline description in README Pipeline description in README Mar 26, 2025
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github-actions bot commented Mar 26, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 1824be0

+| ✅ 194 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  13 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • nextflow_config - Config manifest.version should not contain dev for a release: 1.0dev
  • version_consistency - manifest.version was not numeric: 1.0dev!
  • included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ 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: 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 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 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 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:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-26 13:10:57

@Patricie34 Patricie34 changed the base branch from master to dev March 26, 2025 13:41
@matrulda matrulda mentioned this pull request Mar 26, 2025
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@torigiffin
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I had some other ideas of stuff that would be helpful for beginners!

##Introduction:

  • I think it would be nice to add a code block of the -profile test command instead of just the flag in the text

##Usage:

I would say run directory not run dir

tags: I would say such as lanes, projects, etc.

  • tags are never explained as the like "marker" for the pipeline

Updating the pipeline:
Maybe this would be helpful near the beginning? nextflow pull nf-core/seqinspector maybe put the version command near it so you can do it all together

##Parameters:
--multiqc__title
"MultiQC report title for all generated reports"

I think the --fasta parameter being mandatory if there is no --genome is hidden in the help text on parameters page. I think somewhere in usage or intro it should say one or the other is necessary

matrulda
matrulda reviewed Mar 26, 2025
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@Patricie34 @matrulda
Update README.md
6d60c9d 
Co-authored-by: Matilda Åslin <[email protected]>
pontushojer
pontushojer reviewed Jul 9, 2025
View reviewed changes
README.md
Comment on lines +35 to +37
3. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
4. Contamination QC ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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Suggested change
3. Sequence statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
4. Contamination QC ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
5. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
3. Report read counts and lengths statistics ([`SeqFu Stats`](https://github.com/telatin/seqfu2))
4. Screen reads against references ([`FastQ Screen`](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/))
5. Compile QC results into report ([`MultiQC`](http://multiqc.info/))

Hi, Here are some suggestions for updated descriptions that aim to clarify further what each tool does and present them more succinctly. I also changed the MultiQC one as "raw reads" is not accurate when we now have subsampling. Let me know what you think! :)

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@Patricie34 @torigiffin @matrulda @pontushojer