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Fix --three_prime_clip_r{1,2} parameter documentation (fixes #1382) #1383

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merged 6 commits into from Feb 6, 2024
Merged

Fix --three_prime_clip_r{1,2} parameter documentation (fixes #1382) #1383

merged 6 commits into from Feb 6, 2024

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tdanhorn
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PR checklist

  • This comment contains a description of changes (with reason).
    Changed /nextflow_schema.json to correct the FastP parameter corresponding to --three_prime_clip_r{1,2}
  • 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/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 --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 Jan 25, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e5f48b7

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-06 09:59:22

@tdanhorn tdanhorn linked an issue Jan 25, 2024 that may be closed by this pull request
Typo in --three_prime_clip_r{1,2} parameter documentation #1382
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FriederikeHanssen
FriederikeHanssen reviewed Jan 25, 2024
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Thank you for fixing this <3 . Can you update the Changelog?

@maxulysse
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@nf-core-bot fix linting pretty please

@maxulysse
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Sorry about that.
And no worries, it's valid

@tdanhorn
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tdanhorn commented Feb 6, 2024

I updated the CHANGELOG to add this PR and fix the number of the previous PR.

FriederikeHanssen
FriederikeHanssen previously approved these changes Feb 6, 2024
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Thank you @tdanhorn 🚀

@maxulysse
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this issue is caused by a more recent prettier version compared to the one used in pre-commit.

maxulysse
maxulysse previously approved these changes Feb 6, 2024
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maxulysse
maxulysse reviewed Feb 6, 2024
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CHANGELOG.md Show resolved Hide resolved
@maxulysse maxulysse merged commit 8fba43d into nf-core:dev Feb 6, 2024
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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Typo in --three_prime_clip_r{1,2} parameter documentation
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@tdanhorn @maxulysse @FriederikeHanssen @nf-core-bot