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Add FASTQ linting during preprocessing #1461

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merged 24 commits into from
Dec 3, 2024
Merged

Add FASTQ linting during preprocessing #1461

merged 24 commits into from
Dec 3, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Dec 2, 2024 •
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Workflow-level implementation of nf-core/modules#7123.

This is a reworking of @oligomyeggo's work in #1453, I needed permissions to fix up the test suite etc and couldn't push to that fork.

We also forgot to bump versions after the last release, doing that here too.

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/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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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github-actions bot commented Dec 2, 2024

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 @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq 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 nf-core/rnaseq 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!

@pinin4fjords pinin4fjords changed the base branch from master to dev December 2, 2024 16:28
@pinin4fjords pinin4fjords changed the title Swf rnaseq prepro lint Add FASTQ linting during preprocessing Dec 2, 2024
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github-actions bot commented Dec 2, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b8b5aa2

+| ✅ 187 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 base.config: Check the defaults for all processes
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-03 20:59:07

@pinin4fjords pinin4fjords mentioned this pull request Dec 3, 2024
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@pinin4fjords pinin4fjords mentioned this pull request Dec 3, 2024
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@pinin4fjords pinin4fjords linked an issue Dec 3, 2024 that may be closed by this pull request
Check FASTQ files after each preprocessing step (Inconsistent sequence and quality lengths in FASTQ files created by SortMeRNA) #1456
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maxulysse
maxulysse approved these changes Dec 3, 2024
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I would have been more specific with the params
skip_linting seems a bit too generic to me, but PR is good

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I would have been more specific with the params skip_linting seems a bit too generic to me, but PR is good

I thought it was consistent in detail with skip_trimming, but happy to take suggestions if you have specific feedback. Will merge for now

@pinin4fjords pinin4fjords merged commit 0247f7b into dev Dec 3, 2024
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@pinin4fjords pinin4fjords deleted the swf_rnaseq_prepro_lint branch December 3, 2024 23:12
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@maxulysse maxulysse maxulysse approved these changes

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