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Update utility subworkflows #273

Merged
merged 3 commits into from
Feb 15, 2024
Merged

Update utility subworkflows #273

merged 3 commits into from
Feb 15, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Feb 13, 2024 •
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Update utility subworkflows to match latest version.
I haven't updated the CHANGELOG since so much has changed already.

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/fetchngs 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).

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github-actions bot commented Feb 13, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 302694c

+| ✅ 149 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: 1.12.0

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-14 13:38:32

@maxulysse
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UTILS_NFCORE_PIPELINE now take an arg, I'm surprized there was no failure there...

@maxulysse maxulysse changed the title Upate utility subworkflows Update utility subworkflows Feb 13, 2024
@drpatelh
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CHANGELOG? Otherwiese good to go.

@adamrtalbot adamrtalbot merged commit 125dbb1 into nf-core:dev Feb 15, 2024
22 checks passed
@adamrtalbot adamrtalbot deleted the module_updates branch February 15, 2024 14:20
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@maxulysse maxulysse maxulysse approved these changes

@drpatelh drpatelh drpatelh approved these changes

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@adamrtalbot @maxulysse @drpatelh