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qcatch: Add doublet detection test#10126

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DongzeHE merged 3 commits intonf-core:masterfrom
an-altosian:qcatch-doublet-test
Feb 26, 2026
Merged

qcatch: Add doublet detection test#10126
DongzeHE merged 3 commits intonf-core:masterfrom
an-altosian:qcatch-doublet-test

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@an-altosian an-altosian commented Feb 22, 2026

Address nf-test concerns for the qcatch module in #10125.

Summary

  • Add test_qcatch - remove_doublets test that exercises the --remove_doublets code path requiring scikit-image
  • Uses file size > 0 assertions for non-deterministic outputs (scrublet results vary across CPU architectures due to BLAS/LAPACK differences)
  • Snapshots versions.yml for deterministic validation
  • Follows nf-core assertion guidelines for handling unstable content

Addresses review feedback from @mashehu on #10125.

Test plan

  • All 3 tests pass locally with Docker (base, doublet, stub)
  • CI passes all shards (docker, conda, singularity)

🤖 Generated with Claude Code

@an-altosian
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@mashehu any comments?

- Add test_qcatch - remove_doublets test exercising the --remove_doublets
  code path. Uses file size > 0 assertions for non-deterministic outputs
  and snapshots versions.yml.
- Update qcatch to 0.2.11 (bundles scikit-image, removes need for
  separate scikit-image pip dependency)
- Update container images to 0.2.11
- Use https link for Singularity container

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@DongzeHE DongzeHE enabled auto-merge February 26, 2026 15:30
@DongzeHE DongzeHE added this pull request to the merge queue Feb 26, 2026
Merged via the queue into nf-core:master with commit cd518d4 Feb 26, 2026
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an-altosian added a commit to an-altosian/scrnaseq that referenced this pull request Feb 26, 2026
- Bump qcatch to 0.2.11 (scikit-image now bundled in package)
- New container with python 3.14.3
- Add doublet detection test (remove_doublets) with dedicated config
- Add versions yaml assertion to main test
- Update snapshots and modules.json SHA

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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3 participants