feat(qpx): flatten QPX export output into qpx/ (drop qpx_output/ subfolder)#100
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…older) Publish the QPX Parquet dataset files and the .h5mu MuData file directly under results/qpx/, removing the intermediate qpx/qpx_output/ level. - modules/bigbio/qpx: emit the dataset as qpx_output/* files instead of the qpx_output/ directory (mirrors bigbio/nf-modules#39), so publishDir can flatten the files. A directory output and the sibling .h5mu race in publishDir and one is dropped, so flattening config-only is not reliable. - conf/modules/shared.config: QPX_EXPORT publishDir now strips the qpx_output/ prefix via saveAs (tokenize('/').last()) and publishes to qpx/. Pin bump for modules.json follows once bigbio/nf-modules#39 lands on main. Docs (output.md, usage.md) already describe the flat results/qpx/ layout.
Update modules.json qpx git_sha to the merge commit of bigbio/nf-modules#39, which emits the QPX dataset as qpx_output/* files. Keeps nf-core check_local_copy green for the flattened output change.
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Problem
When
--enable_qpx_exportis set, results were split across two levels:The intermediate
qpx_output/subfolder is unnecessary — everything should live directly underqpx/.Fix
Publish the QPX Parquet dataset files and the
.h5muflat underresults/qpx/:This already matches what
docs/output.mdanddocs/usage.mddescribe.Why this needs a module change (not config-only)
The module emitted the dataset as a directory (
qpx_output/). Publishing a directory output and the sibling.h5mufile into the sameqpx/folder makes Nextflow'spublishDirrace — one of them is silently dropped (verified with stub runs). So the module must emit the dataset as files (qpx_output/*), whichpublishDircan then flatten.Changes
modules/bigbio/qpx/{main.nf,meta.yml}:qpx_datasetoutput is nowqpx_output/*(files) instead of theqpx_output/directory. Mirrors upstream fix(qpx): emit dataset as qpx_output/* files instead of a directory nf-modules#39 (merged);modules.jsonpin bumped to that commit.conf/modules/shared.config:QPX_EXPORTpublishDirstrips theqpx_output/prefix viasaveAs { ... tokenize('/').last() }and publishes toqpx/.Validation
results/qpx/{<prefix>.parquet, <prefix>.h5mu}, noqpx_output/.nf-core pipelines lint: 0 failures (includingcheck_local_copyafter the pin bump).mudata/versionsoutputs and the module stub test (qpx_dataset.size() == 1) are unchanged.