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feat: add stub blocks for QC & filtering modules (#4570)#11350

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HReed1 wants to merge 1 commit intonf-core:masterfrom
HReed1:stub/qc-filtering
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feat: add stub blocks for QC & filtering modules (#4570)#11350
HReed1 wants to merge 1 commit intonf-core:masterfrom
HReed1:stub/qc-filtering

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@HReed1 HReed1 commented Apr 28, 2026

Adds deterministic stub: blocks and corresponding -stub nf-test cases for QC & filtering modules, as part of the ongoing effort to resolve #4570. Split from the original monolithic #11323 per reviewer feedback.

Each stub generates placeholder output files matching the module's output channel declarations:

  • Plain-text outputs use touch
  • Compressed (.gz) outputs use echo | gzip >
  • versions.yml blocks are copied 1:1 from the script block

Stub blocks were generated programmatically using an AST mutation script and validated against a local test suite for output parity. For full documentation on the tooling, conventions, and methodology used, see the Nextflow contribution docs.

Modules affected (5)

  • fastqscan
  • filtlong
  • prinseqplusplus
  • pycoqc
  • rasusa

Tests

All modules include -stub nf-test cases with assertAll() + snapshot(process.out).match(). Snapshots generated locally via nf-test --update-snapshot.

PR checklist

Contributes to #4570. Split from #11323.

  • This comment contains a description of changes (with reason).
  • Stub tests added for all modules.
  • Follows the module conventions in the contribution docs.
  • Remove all TODO statements.
  • Follow the naming conventions.

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HReed1 commented Apr 28, 2026

@nf-core-bot fix linting

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HReed1 commented Apr 30, 2026

Closing legacy batched PR in favor of atomic 1-PR-per-module approach with topic channel migration, as requested by reviewers.

@HReed1 HReed1 closed this Apr 30, 2026
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[FEATURE] Add stub support to every module

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