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Add modules #6

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Add modules #6

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kedhammar
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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).

@kedhammar kedhammar added the enhancement New feature or request label Mar 19, 2024
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github-actions bot commented Mar 19, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b883059

+| ✅ 168 tests passed       |+
!| ❗  25 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 main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • 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: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • 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.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-22 07:33:55

@kedhammar kedhammar mentioned this pull request Mar 19, 2024
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@kedhammar
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Addresses #8

@alneberg
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what's the usecase for clumpify again? Is it to produce more compressed fastqs or something else?

@kedhammar
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what's the usecase for clumpify again? Is it to produce more compressed fastqs or something else?

https://nf-co.re/modules/bbmap_clumpify

Main use case for us seems to be deduplication

@alneberg
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I would say skip clumpify at this point and maybe give a try to run fastp inside the main.nf as well? It should be ran for any file so fairly similar to fastqc I would imagine?

@Aratz
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Aratz commented Mar 21, 2024

fastp is used in nf-core/demultiplex, see here for inspiration: https://github.com/nf-core/demultiplex/blob/aa4d93673a4e04b1daf7b4bd71269d6054275534/workflows/demultiplex.nf#L199

@kedhammar kedhammar closed this May 13, 2024
@kedhammar kedhammar deleted the add-modules branch May 13, 2024 12:35
@kedhammar
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This PR is a bit too broad in scope, so I'm closing it. Please see #8 for inspiration.

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3 participants
@kedhammar @alneberg @Aratz