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Bump lots of modules so that conda versions have arm builds #1422

Merged
merged 17 commits into from
Oct 21, 2024
Merged

Bump lots of modules so that conda versions have arm builds #1422

merged 17 commits into from
Oct 21, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Oct 21, 2024 •
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I just did a complete module update, so this is pulling in everything (e.g. meta.yml reformatting applied across nf-core). But I'm really mostly after the new versions with associated ARM builds.

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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github-actions bot commented Oct 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9078e0f

+| ✅ 186 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 2024-10-21 17:13:36

@pinin4fjords
Update prepare_genome snaps
6739fbd
@pinin4fjords
Update align_star snaps
75fad6f
@pinin4fjords
Update quantify_rsem snaps
a036f5d
@pinin4fjords
[skip ci] First batch of pipeline test updates
5dd65b9
@pinin4fjords
[skip ci] Update subworkflow snaps due to patch on module
7568b2d
@pinin4fjords
[skip ci] bump remove_ribo_rna snaps
c3e0618
@pinin4fjords
Merge branch 'bump_modules_for_arm' of https://github.com/nf-core/rnaseq
aa01883 
 into bump_modules_for_arm
@pinin4fjords
[skip ci] Update snaps for --pseudo_aligner salmon --skip_qc --skip_a…
206c792 
…lignment
@pinin4fjords
[skip ci] update star_rsem pipeline snaps
9f9c8b1
@pinin4fjords
Merge branch 'bump_modules_for_arm' of https://github.com/nf-core/rnaseq
e52596b 
 into bump_modules_for_arm
@pinin4fjords
[skip ci] update pipeline tests for skip_qc
102dc63
@pinin4fjords
Merge branch 'bump_modules_for_arm' of https://github.com/nf-core/rnaseq
5508eb6 
 into bump_modules_for_arm
@pinin4fjords
update skip_trimming snaps
a9dc3dd
@pinin4fjords
update changelog
787ab18
maxulysse
maxulysse approved these changes Oct 21, 2024
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just minor comments

@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit a97256b into dev Oct 21, 2024
166 checks passed
@pinin4fjords pinin4fjords deleted the bump_modules_for_arm branch October 21, 2024 18:23
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@maxulysse maxulysse maxulysse approved these changes

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