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Switch to genomecov from nf-core #1234

Merged
merged 11 commits into from
Mar 6, 2024
Merged

Switch to genomecov from nf-core #1234

merged 11 commits into from
Mar 6, 2024

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pinin4fjords
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@pinin4fjords pinin4fjords commented Mar 5, 2024 •
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Moving existing bedtools genomecov to use nf-core module.

The local module had more baked in options and ran twice for forward and reverse. I've moved things to ext.args where necessary and ran the nf-core module twice, once forward and once reverse.

Also sneaking in a tiny bbsplit fix to remove a debugging line I'd left in.

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/rnaseq 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>).
  • 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).

@maxulysse
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workflows/rnaseq/main.nf:
	653: Trailing whitespace

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github-actions bot commented Mar 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cbb9d53

+| ✅ 169 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   7 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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!

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-05 19:30:06

@pinin4fjords pinin4fjords force-pushed the bedtools_genomecov_from_nfcore branch from 233eb55 to e667765 Compare March 5, 2024 16:39
@pinin4fjords pinin4fjords changed the title Switch to genomecov from nf-core (with separate sort) Switch to genomecov from nf-core Mar 5, 2024
@pinin4fjords pinin4fjords linked an issue Mar 6, 2024 that may be closed by this pull request
Migrate bedtools/genome_cov to nf-core/modules #1161
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@pinin4fjords pinin4fjords mentioned this pull request Mar 6, 2024
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@pinin4fjords pinin4fjords merged commit 14c8698 into dev Mar 6, 2024
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@pinin4fjords pinin4fjords deleted the bedtools_genomecov_from_nfcore branch March 6, 2024 11:20
@pinin4fjords pinin4fjords mentioned this pull request Mar 6, 2024
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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Migrate bedtools/genome_cov to nf-core/modules
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@pinin4fjords @maxulysse @adamrtalbot