8000 Skip prediction if fasta_output flag is set by axelwalter · Pull Request #286 · nf-core/epitopeprediction · GitHub
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Skip prediction if fasta_output flag is set #286

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Merged
merged 3 commits into from
Jun 3, 2025
Merged

Skip prediction if fasta_output flag is set #286

merged 3 commits into from
Jun 3, 2025

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axelwalter
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@axelwalter axelwalter commented Jun 2, 2025 •
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The --fasta_output flag allows for the generation of FASTA files directly from input VCF variants. Since this does not require MHC binding prediction, this PR adds a conditional to skip the prediction steps.

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/epitopeprediction 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: 3.2.1.
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.

jonasscheid
jonasscheid reviewed Jun 2, 2025
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jonasscheid
jonasscheid requested changes Jun 2, 2025
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jonasscheid
jonasscheid requested changes Jun 2, 2025
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Thanks! :) Only some minor changes.

@axelwalter
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Thanks for the review! The recent addresses your suggestions.

jonasscheid
jonasscheid reviewed Jun 3, 2025
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