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@iraiosub iraiosub commented Apr 4, 2025

Changes to test_full config so running the pipeline with -profile test_full runs beyond UMI deduplication:

  • updated FASTA and GTF paths to those hosted on Ensembl instead of igenomes. These are downloaded at runtime (tested).
  • renamed UMI related params to match those in nextflow.config and enabled UMI extraction (so now UMI collapse doesn't fail)
  • despite these changes that help the test_full progress further, test_full still fails in later steps at processes related to consensus peak analyses

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/clipseq 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).
  • 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).

@iraiosub iraiosub added the enhancement Improvement for existing functionality label Apr 4, 2025
@iraiosub iraiosub requested a review from CharlotteAnne April 4, 2025 16:05
@iraiosub iraiosub self-assigned this Apr 4, 2025
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iraiosub commented Apr 9, 2025

closing this PR, as these changes are also implemented in #166

@iraiosub iraiosub closed this Apr 9, 2025
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