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patch sortmerna to 4.3.7 for ARM compatibility #1424

Merged
merged 4 commits into from
Oct 22, 2024
Merged

patch sortmerna to 4.3.7 for ARM compatibility #1424

merged 4 commits into from
Oct 22, 2024

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pinin4fjords
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This is done with a patch, since it needs the sortmerna from the seqera conda channel. 4.3.7 in Bioconda is non-functional (illegal instruction errors), and it's not yet in conda-forge as authors apparently intended.

At such time as sortmerna authors do their thing, and this appears in conda-forge, the nf-core module can be properly updated and we can remove the patch 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>).
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  • Output Documentation in docs/output.md is updated.
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  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Oct 22, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 82dfdf2

+| ✅ 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 2024-10-22 12:29:35

@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit 3671d59 into dev Oct 22, 2024
34 checks passed
@pinin4fjords pinin4fjords deleted the bump_sortmerna branch October 22, 2024 12:53
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@maxulysse maxulysse maxulysse approved these changes

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