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skip over empty fastqs after demultiplex #165

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wants to merge 33 commits into from
Closed

skip over empty fastqs after demultiplex #165

wants to merge 33 commits into from

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glichtenstein
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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/demultiplex 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>).
  • 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).

@glichtenstein glichtenstein requested a review from a team as a code owner January 8, 2024 19:08
@glichtenstein glichtenstein requested review from matthdsm and removed request for a team January 8, 2024 19:08
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github-actions bot commented Jan 8, 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 @glichtenstein,

It looks like this pull-request is has been made against the glichtenstein/demultiplex 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 glichtenstein/demultiplex 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!

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github-actions bot commented Jan 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aa54803

+| ✅ 160 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowDemultiplex.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-12 20:42:48

maxulysse
maxulysse reviewed Jan 9, 2024
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subworkflows/nf-core/bcl_demultiplex/main.nf Outdated
Comment on lines 78 to 88
process WriteInvalidFastqPaths {
output:
file("invalid_fastqs.txt") into ch_failed_fastqs_file

publishDir "${params.outdir}", mode: 'copy'

script:
"""
cat ${invalid_fastqs_ch.collect().join('\n')} > invalid_fastqs.txt
"""
}
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I think we can do that outside a process with a collectFile operator

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Agreed, that's one way to do it, but I think it can just be native Nextflow.

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Thanks for the review guys! Very good point, I will switch to collectFile and test again.

@glichtenstein glichtenstein changed the base branch from master to dev January 9, 2024 16:06
@glichtenstein glichtenstein changed the title SDP-2057 debug nf-core/demultiplex line 125 skip over empty fastqs after demultiplex Jan 9, 2024
@glichtenstein glichtenstein marked this pull request as draft January 9, 2024 20:09
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I will work on this more, I still need to do more tests. I'm considering making that behaviour for skipping emtpy fastqs optional. Should I close the pull request or can I leave it as a draft? Thanks for the reviews.

@Aratz
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Aratz commented Jan 10, 2024

I'd leave it as draft, so that everybody can see what the status is with this issue and maybe not start something else from scratch.

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@edmundmiller edmundmiller edmundmiller left review comments

@maxulysse maxulysse maxulysse left review comments

@matthdsm matthdsm Awaiting requested review from matthdsm matthdsm is a code owner automatically assigned from nf-core/demultiplex

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@glichtenstein @Aratz @maxulysse @edmundmiller @robsyme