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Add full-size test and finer seqdepth grid - #74

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MaximilianStammnitz merged 2 commits into
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test-full-gid1a
Oct 7, 2026
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MaximilianStammnitz merged 2 commits into
devfrom
test-full-gid1a

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@BenjaminWehnert1008

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test_full now runs the GID1A dataset from ENA (PRJEB110196), and the seqdepth rarefaction uses a geometric depth grid instead of 40 even 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/dmscore 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).

test_full now runs the GID1A dataset from ENA (PRJEB110196), and the seqdepth rarefaction uses a geometric depth grid instead of 40 even steps.
@MaximilianStammnitz

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Linked to #68 😇

Comment thread conf/test_full.config Outdated
The GID1A AlphaFold model now lives on the deepmutscan branch of nf-core/test-datasets instead of in assets/.
@BenjaminWehnert1008

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CI now depends on nf-core/test-datasets#1972. Will fail until test datasets got merged.

@MaximilianStammnitz
MaximilianStammnitz merged commit 7d4c6d0 into dev Oct 7, 2026
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@MaximilianStammnitz
MaximilianStammnitz deleted the test-full-gid1a branch October 7, 2026 12:04
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2 participants