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Removed extra_fastp_args and replaced it with fastp_extra_args #81

Merged
merged 1 commit into from
Oct 29, 2024
Merged

Removed extra_fastp_args and replaced it with fastp_extra_args #81

merged 1 commit into from
Oct 29, 2024

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GallVp
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@GallVp GallVp commented Oct 29, 2024

PR checklist

  • Removed extra_fastp_args and replaced it with fastp_extra_args. Closes Rename extra_fastp_args to fastp_extra_args #75
  • 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
  • Make sure your code lints (nf-core 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>).
  • 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).

@GallVp GallVp linked an issue Oct 29, 2024 that may be closed by this pull request
Rename extra_fastp_args to fastp_extra_args #75
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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6c1e2a7

+| ✅ 101 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: assets/nf-core-genepal_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genepal_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genepal_logo_dark.png
  • nextflow_config - nextflow_config
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genepal_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genepal_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genepal_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genepal/genepal/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-29 02:19:55

@GallVp GallVp merged commit 0365f6e into dev Oct 29, 2024
7 checks passed
@GallVp GallVp deleted the rename/arg branch November 6, 2024 05:56
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Rename extra_fastp_args to fastp_extra_args
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