feat(dda): refine OpenMS -out_qpx into clean QPX, replace mzTab as published artifact - #725
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feat(dda): refine OpenMS -out_qpx into clean QPX, replace mzTab as published artifact#725ypriverol wants to merge 1 commit into
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…blished artifact Add a QPX_CONVERT step to the DDA LFQ and TMT workflows that runs the qpx tool (qpxc convert openms) over the OpenMS -out_qpx output + the companion consensusXML + the SDRF, producing the final clean QPX dataset (canonical channel labels, run/sample/ontology/provenance/dataset tables, MuData) at parity with the DIA-NN (quantmsdiann) path. - new module modules/local/qpx/qpx_convert/main.nf - wire QPX_CONVERT into workflows/lfq.nf and workflows/tmt.nf - final_result (fed to pmultiqc) now emits the QPX dataset instead of the mzTab - MSSTATS already consumes consensusXML, not mzTab -- no change needed there - nextflow.config: qpx_version + accession params DRAFT: blocked on the qpx tool release + its BioContainer. See OpenMS#9817 for the upstream -out_qpx labelling fixes.
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What & why
Replace the mzTab with a clean QPX as the DDA pipeline's published quantification artifact.
OpenMS
ProteomicsLFQ/IsobaricWorkflowalready emit a partial QPX via-out_qpx(psm/feature/pg parquet), but that output (a) carries raw channel labels (run filename / bare index) and (b) lacks the metadata tables (run, sample, ontology, provenance, dataset) and the MuData (.h5mu) view. This PR adds aQPX_CONVERTstep that runs theqpxtool (qpxc convert openms) over-out_qpx+ the companionconsensusXML+ the SDRF to produce the final QPX — canonical TMT/iTRAQ/LFQ channel labels, full metadata, and MuData — bringing the DDA path to parity with the DIA-NN (quantmsdiann) QPX.Changes
modules/local/qpx/qpx_convert/main.nf—QPX_CONVERTprocess (qpxc convert openms --qpx-dir … --consensusxml … --sdrf-file … --output-folder …).workflows/lfq.nf— runQPX_CONVERTafterPROTEOMICSLFQ;final_resultnow emits the QPX dataset.workflows/tmt.nf— runQPX_CONVERTafterISOBARIC_WORKFLOW;final_resultnow emits the QPX dataset.nextflow.config—qpx_version,accessionparams.mzTab removal
final_result(the channel fed intopmultiqcand published) switches from*_openms.mzTabto the QPX dataset folder. This is safe because:MSSTATS_CONVERTER), not the mzTab.The OpenMS modules still produce the mzTab (
-out_mzTab) for now; a follow-up can drop-out_mzTabfromproteomicslfq/isobaric_workflowonce we confirm nothing downstream reads it.Blocked on (DRAFT)
biocontainers/qpx:${params.qpx_version}; that image does not exist yet. Set the real tag once qpx is released/containerised..h5muis usable.Notes / assumptions
file(params.input)— correct for SDRF-driven DDA runs (the reanalysis path). Sample-sheet-only inputs have no SDRF and would need a guard.-out_qpxlabelling issues tracked in OpenMS#9817;QPX_CONVERTrelabels downstream from the consensusXML/SDRF until those land.