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Updated modules and subworkflows #259

Merged
merged 4 commits into from
Sep 17, 2024
Merged

Updated modules and subworkflows #259

merged 4 commits into from
Sep 17, 2024

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nschcolnicov
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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>).
  • 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 Aug 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ad66840

+| ✅ 190 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.5.1
  • 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 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-29 12:08:29

@nschcolnicov
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@apeltzer There seems to be an issue with the new module from MultiQC, when using the latest containers kraken report does not get added to it. Already reported the issue in MultiQC:
MultiQC/MultiQC#2801

@nschcolnicov
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sgdemux and fqtk now sometimes generate an additional task, possibly retrying a failed execution, not sure because I haven't been able to reproduce when running locally

@apeltzer
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MQC 1.25 (see PR nf-core/modules#6655 (comment)) should fix this

@apeltzer apeltzer changed the base branch from dev to modules-updates September 17, 2024 14:28
@apeltzer apeltzer marked this pull request as ready for review September 17, 2024 14:28
@apeltzer apeltzer requested a review from a team as a code owner September 17, 2024 14:28
@apeltzer apeltzer requested review from glichtenstein and removed request for a team September 17, 2024 14:28
@apeltzer apeltzer merged commit 8c8fec3 into nf-core:modules-updates Sep 17, 2024
8 of 9 checks passed
@apeltzer
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Merging this into a branch on nf-core already 👍🏻

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

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@nschcolnicov @apeltzer