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Update FastQC and UMItools modules #1138

Merged
merged 9 commits into from
Dec 8, 2023
Merged

Update FastQC and UMItools modules #1138

merged 9 commits into from
Dec 8, 2023

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mahesh-panchal
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@mahesh-panchal mahesh-panchal commented Dec 8, 2023 •
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Updates FASTQC and UMITOOLS modules that have new commands for version strings to fix #1103

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>).
  • 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).

@mahesh-panchal mahesh-panchal marked this pull request as draft December 8, 2023 10:21
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github-actions bot commented Dec 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ed2b8aa

+| ✅ 145 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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 WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-08 15:42:54

@mahesh-panchal mahesh-panchal marked this pull request as ready for review December 8, 2023 10:44
@maxulysse
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@mahesh-panchal Can you update the modules with nf-core/modules#4520 too while we're at it?

maxulysse
maxulysse reviewed Dec 8, 2023
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@mahesh-panchal
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@mahesh-panchal Can you update the modules with nf-core/modules#4520 too while we're at it?

Done.

@mahesh-panchal
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Wonderful ... subworkflow was changed and breaks stuff.

@maxulysse
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sorry about that

@mahesh-panchal
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No problem. Sorting it.

@maxulysse
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No problem. Sorting it.

which subworkflows was it?
I'd like to checkout the PR for this breaking change

@mahesh-panchal
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BAM_RSEQC subworkflow. meta.yml also doesn't match the channel names.

@maxulysse
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BAM_RSEQC subworkflow. meta.yml also doesn't match the channel names.

I don't see much happening there https://github.com/nf-core/modules/blame/master/subworkflows/nf-core/bam_rseqc/meta.yml

so I'm guessing issue is coming from here

@mahesh-panchal
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Something's broken with that subworkflow. Not having inner_distance in the modules causes the subworkflow to break.

maxulysse
maxulysse approved these changes Dec 8, 2023
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Thank you so much @mahesh-panchal for committing so much to this PR

@mahesh-panchal mahesh-panchal merged commit f55a154 into nf-core:dev Dec 8, 2023
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@pinin4fjords pinin4fjords mentioned this pull request Jan 3, 2024
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@drpatelh drpatelh mentioned this pull request Jan 3, 2024
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@maxulysse maxulysse maxulysse approved these changes

@MatthiasZepper MatthiasZepper Awaiting requested review from MatthiasZepper

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@mahesh-panchal @maxulysse