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Factor out preprocessing #1342

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merged 12 commits into from
Jul 17, 2024
Merged

Factor out preprocessing #1342

merged 12 commits into from
Jul 17, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Jul 16, 2024 •
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Finally move preprocessing logic to the subworkflow, which I factored out of RNAseq to use in Riboseq.

I've had to update the subworkflow itself to incorporate some improvements related to strandedness, which we'd made in the meantime nf-core/modules#5982, so that will need merging first.

Edit: also nf-core/modules#5988

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 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).

@pinin4fjords pinin4fjords marked this pull request as draft July 16, 2024 11:08
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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 @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 July 16, 2024 11:08
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github-actions bot commented Jul 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5507a6d

+| ✅ 173 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 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 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 2.14.1
  • Run at 2024-07-17 13:37:11

@pinin4fjords pinin4fjords mentioned this pull request Jul 16, 2024
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@pinin4fjords pinin4fjords marked this pull request as ready for review July 17, 2024 11:12
maxulysse
maxulysse reviewed Jul 17, 2024
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workflows/rnaseq/main.nf
Comment on lines +711 to 719
ch_name_replacements = ch_fastq
.filter{ meta, reads ->
reads.size() == 1
}
.map{ meta, reads ->
def name1 = file(reads[0]).simpleName + "\t" + meta.id + '_1'
def name1 = file(reads[0][0]).simpleName + "\t" + meta.id + '_1'
if (reads[1] ){
def name2 = file(reads[1]).simpleName + "\t" + meta.id + '_2'
def name2 = file(reads[0][1]).simpleName + "\t" + meta.id + '_2'
return [ name1, name2 ]
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What's this whole change about?

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It's because I'm using ch_fastq directly (since the one with single and multiple branches is moved to the subworkflow). So these are now tuples output by groupTuple requiring the double index:

[[foo.fastq.gz,bar.fastq.gz]]

maxulysse
maxulysse approved these changes Jul 17, 2024
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I love this <3

@pinin4fjords
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I love this <3

Glad to hear- especially since you were skeptical about the subworkflow!

@pinin4fjords pinin4fjords merged commit 5bd04b4 into dev Jul 17, 2024
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@pinin4fjords pinin4fjords deleted the factor_out_preprocessing branch July 17, 2024 15:30
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@maxulysse maxulysse maxulysse approved these changes

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