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Make genomic FASTA input optional #1490

Merged
merged 26 commits into from
Jan 22, 2025
Merged

Make genomic FASTA input optional #1490

merged 26 commits into from
Jan 22, 2025

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pinin4fjords
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@pinin4fjords pinin4fjords commented Jan 21, 2025 •
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Edits to various components to allow operation without a FASTA file. Required an upstream change to the Salmon indexing module. Add documentation to make clear that providing a genome fasta is still preferable with Salmon to exploit decoy-aware indexing.

Closes #688

I've temporarily disabled the 'latest' testing to work around nextflow-io/nextflow#5686 until the template is updated.

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 pipelines 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).

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Jan 21, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 21eb5ad

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 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 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!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-22 16:47:47

@pinin4fjords pinin4fjords changed the title Optional fasta Make genomic FASTA input optional Jan 21, 2025
@pinin4fjords pinin4fjords mentioned this pull request Jan 22, 2025
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maxulysse
maxulysse reviewed Jan 22, 2025
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maxulysse
maxulysse approved these changes Jan 22, 2025
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minor comments

pinin4fjords
pinin4fjords commented Jan 22, 2025
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pinin4fjords
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@pinin4fjords pinin4fjords merged commit 0b70ad7 into dev Jan 22, 2025
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