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@suhrig suhrig commented Jun 27, 2025

When the pipeline is launched with the parameter --genome set, the FastA file is normally obtained from the igenomes.config file. However, the pipeline complains that --fasta is not set in this situation. This PR changes the parameter validation to require that only --genome or --fasta be set.

Note: Linting currently fails with FileNotFoundError: [Errno 2] No such file or directory: 'tests/nextflow.config', but this has nothing to do with this PR.

PR checklist

  • This comment contains a description of changes (with reason).
  • 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.
  • CHANGELOG.md is updated.

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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.

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2 participants