fix(pridepy): drop output/ subdir, write to workDir

[Shen-YuFei]

Pull Request

Description

Address review on #31: mkdir -p output and cd output are unnecessary because Nextflow already runs each task in its own workDir; the explicit output/ subdirectory wraps the tool call in dead weight. Switch the module to write outputs directly to the workDir and let downstream pipelines glob via modules.config.

• main.nf
  • Drop mkdir -p output + cd output wrapper from script; pridepy now writes to the workDir root.
  • Replace tuple val(meta), path(output/) with two emit channels matching nf-modules style (cf. THERMORAWFILEPARSER):
    • spectra — *.{raw,mzML,mzML.gz,mgf,d.tar,d.tar.gz,d.zip,dia,wiff,wiff.scan}, optional: true
    • checksums — *-checksum.tsv, optional: true
  • Stub now gates -checksum.tsv creation on --checksum-check in task.ext.args so stub behaviour matches production.
• meta.yml: sync output schema (download_dir -> spectra + checksums).
• tests/main.nf.test + tests/nextflow.config: expand stub coverage to two cases (no checksum / with --checksum-check); assertions cover spectra / checksums / versions size and snapshots.

Verified locally:

nf-test test modules/bigbio/pridepy/tests/main.nf.test
Test [aa2c172f] 'Should run stub mode (no checksum)' PASSED (6.925s)
Test [c50bb176] 'Should run stub mode with --checksum-check' PASSED (6.211s)
SUCCESS: Executed 2 tests in 13.219s

Downstream consumers (quantms, quantmsdiann) will need to drop -o output from task.ext.args and switch from the download_dir directory channel to the spectra file channel.

Checklist

• Module follows nf-core standards
• main.nf includes process definition
• meta.yml includes complete documentation
• environment.yml specifies dependencies
• Tests are included
• Code is formatted (prettier)
• CI checks pass

Module Type

• New module
• Module update
• Bug fix
• Documentation

Related Issues

Refs #31

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[codacy-production]

Up to standards ✅

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[Copilot]

Pull request overview

Updates the bigbio/pridepy Nextflow module to write outputs directly into the task work directory (instead of an output/ subfolder) and aligns emitted outputs and tests with nf-modules conventions.

Changes:

• Removed the mkdir -p output / cd output wrapper so pridepy writes to the workDir root.
• Replaced the single download_dir directory output with two optional emitted channels: spectra and checksums.
• Expanded nf-test coverage to validate stub behavior for both “no checksum” and “with --checksum-check” cases, updating snapshots accordingly.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
modules/bigbio/pridepy/main.nf	Drops output/ subdir usage; emits spectra + checksums (optional) and updates stub to conditionally create checksum output.
modules/bigbio/pridepy/meta.yml	Syncs output schema/documentation from download_dir to spectra + checksums.
modules/bigbio/pridepy/tests/nextflow.config	Adds withName: PRIDEPY_DOWNLOAD to pass module args via ext.args from test params.
modules/bigbio/pridepy/tests/main.nf.test	Adds two stub-mode tests and asserts channel sizes + snapshots for spectra/checksums/versions.
modules/bigbio/pridepy/tests/main.nf.test.snap	Updates snapshots to match new emitted channels and stub outputs.

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