Integrate QPX Parquet and MuData export into workflow

[Shen-YuFei]

PR checklist

• This comment contains a description of changes (with reason).
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.

Description

Integrate QPX (v1.0.2) into the DIA workflow for standardized Parquet + MuData export.

QPX converts DIA-NN results into the QPX Parquet format and generates MuData (.h5mu) files for downstream analysis in the scverse ecosystem.

Changes (16 files)

New module — modules/bigbio/qpx/

• main.nf — QPX_EXPORT process: runs qpxc convert diann + MuData export
• meta.yml — module metadata (input/output channel definitions)
• environment.yml — conda environment spec
• tests/ — nf-test with snapshot

Workflow integration — workflows/dia.nf

• Added QPX_EXPORT step after DIA-NN quantification, gated by params.qpx_export

Configuration

• nextflow.config — new params.qpx_export (default: true) and params.matrix_qvalue
• nextflow_schema.json — registered new parameters
• conf/modules/shared.config — QPX_EXPORT process config
• conf/tests/test_dia_qpx.config — dedicated test profile

CI

• .github/workflows/extended_ci.yml — added test_dia_qpx profile

Docs

• docs/usage.md — QPX export usage and parameters
• docs/output.md — QPX output description
• CHANGELOG.md — added entry

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[Copilot]

Pull request overview

This PR integrates QPX into the DIA workflow to export DIA-NN quantification outputs as a standardized QPX Parquet dataset plus a MuData (.h5mu) artifact for downstream analysis.

Changes:

• Added a new QPX_EXPORT Nextflow module (with nf-test coverage) to run qpxc convert diann and generate a .h5mu.
• Wired QPX_EXPORT into workflows/dia.nf, gated by --enable_qpx_export, and published outputs under ${outdir}/qpx.
• Added a dedicated CI test profile (test_dia_qpx), updated docs, and updated the changelog.

Reviewed changes

Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
workflows/dia.nf	Includes and conditionally runs QPX_EXPORT, emits qpx_dataset and mudata.
nextflow.config	Adds enable_qpx_export default and test_dia_qpx profile entry.
nextflow_schema.json	Adds a schema section for QPX export toggle.
modules/bigbio/qpx/main.nf	New QPX_EXPORT process implementation (QPX convert + MuData export + versions).
modules/bigbio/qpx/meta.yml	Module metadata describing inputs/outputs and tool info.
modules/bigbio/qpx/environment.yml	Conda env definition for QPX execution.
modules/bigbio/qpx/tests/main.nf.test	nf-test coverage for stub mode outputs.
modules/bigbio/qpx/tests/main.nf.test.snap	Snapshot for stub-mode test outputs.
modules/bigbio/qpx/tests/nextflow.config	Test config for module execution (incl. matrix_qvalue).
modules.json	Registers the qpx module source metadata.
conf/modules/shared.config	Publishes QPX_EXPORT outputs to ${outdir}/qpx.
conf/tests/test_dia_qpx.config	New minimal DIA+QPX test profile.
.github/workflows/extended_ci.yml	Adds test_dia_qpx to CI matrix.
docs/usage.md	Documents QPX export usage and the new test profile.
docs/output.md	Documents QPX output artifacts.
CHANGELOG.md	Adds release notes for QPX export and test profile.

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