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Update subworkflow to account for fix to bad argument handling #1470

Merged
merged 4 commits into from
Dec 18, 2024
Merged

Update subworkflow to account for fix to bad argument handling #1470

merged 4 commits into from
Dec 18, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Dec 17, 2024 •
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Deploy the fix in nf-core/modules#7237

I decided to just pass false to the new param, I don't think the read stitching makes sense here.

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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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

maxulysse
maxulysse reviewed Dec 17, 2024
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workflows/rnaseq/main.nf
@@ -155,7 +155,8 @@ workflow RNASEQ {
params.umi_discard_read,
params.stranded_threshold,
params.unstranded_threshold,
params.skip_linting
params.skip_linting,
false
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@maxulysse maxulysse Dec 17, 2024 •
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no params for this?
Just false always?

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I don't really know why it's a module input, I don't think it's a core behaviour of FASTP. I'm struggling to see the use case for it to justify adding a pipeline param and wiring it in.

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Though I can if you really want...

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github-actions bot commented Dec 17, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 11b8670

+| ✅ 188 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 2024-12-18 08:13:01

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ca92fe7

+| ✅ 188 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 2024-12-17 17:33:48

@pinin4fjords pinin4fjords linked an issue Dec 17, 2024 that may be closed by this pull request
The parameter "save_trimmed=true" mistakenly activates merging mode of fastp #1452
Closed
@pinin4fjords pinin4fjords merged commit 06fa117 into dev Dec 18, 2024
32 checks passed
@pinin4fjords pinin4fjords deleted the fix_prepro_arg branch December 18, 2024 12:00
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@maxulysse maxulysse maxulysse approved these changes

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The parameter "save_trimmed=true" mistakenly activates merging mode of fastp
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