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nf-core modules update all with prefix annotation #462

Merged
merged 33 commits into from
Dec 8, 2021
Merged

nf-core modules update all with prefix annotation #462

merged 33 commits into from
Dec 8, 2021

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FriederikeHanssen
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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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

maxulysse
maxulysse approved these changes Dec 6, 2021
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ok for me even if the nf-core lint is not working.
It's made with dev, so I expect it not to be working all the time, I'll make a separate PR to fix the dark/light mode of the logos

@maxulysse maxulysse mentioned this pull request Dec 6, 2021
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github-actions bot commented Dec 7, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5061cbc

+| ✅ 135 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.2.dev0
  • Run at 2021-12-08 19:44:35

maxulysse
maxulysse reviewed Dec 7, 2021
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maxulysse
maxulysse reviewed Dec 7, 2021
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🚀

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review December 8, 2021 20:27
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@maxulysse I think I would leave it as is now and add the mapping workflow together with the UMI sub workflow. The gatk4 modules need upstream updates as discussed, so would also push it to the next PR to allow others to use the updated syntax now

@maxulysse maxulysse merged commit 9094f13 into nf-core:dev Dec 8, 2021
@maxulysse maxulysse mentioned this pull request Dec 8, 2021
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@FriederikeHanssen FriederikeHanssen deleted the update_modules branch July 10, 2023 18:59
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@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@FriederikeHanssen @maxulysse