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Important! Template update for nf-core/tools v3.0.1 #1401

Merged
merged 36 commits into from
Oct 10, 2024
Merged

Important! Template update for nf-core/tools v3.0.1 #1401

merged 36 commits into from
Oct 10, 2024

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Version 3.0.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.0.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.0.1 release page.

@nf-core-bot nf-core-bot mentioned this pull request Oct 9, 2024
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maxulysse
maxulysse reviewed Oct 9, 2024
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maxulysse reviewed Oct 9, 2024
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github-actions bot commented Oct 9, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 386d6bd

+| ✅ 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 3.0.1
  • Run at 2024-10-10 11:07:23

@maxulysse maxulysse mentioned this pull request Oct 10, 2024
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maxulysse
maxulysse reviewed Oct 10, 2024
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maxulysse
maxulysse reviewed Oct 10, 2024
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tests/default.nf.test.snap
@@ -83,14 +83,15 @@
],
[
"genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
"genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
"genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e",
"multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e"
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an upstream fix will come for that (cf nf-core/modules#6762)

maxulysse
maxulysse reviewed Oct 10, 2024
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MULTIQC update had brought tons of filename change.
and I decided not to snapshot images from MultiQC anymore

pinin4fjords
pinin4fjords approved these changes Oct 10, 2024
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Mostly just taking your word for it @maxulysse , but I trust you know what you're up to here

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@maxulysse maxulysse merged commit ea70b71 into dev Oct 10, 2024
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@maxulysse maxulysse deleted the nf-core-template-merge-3.0.1 branch October 10, 2024 11:23
@maxulysse maxulysse mentioned this pull request Oct 16, 2024
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

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@nf-core-bot @maxulysse @pinin4fjords