Guard against running on an empty per-sample input list in tximport/quantify_rsem#12378
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pinin4fjords wants to merge 2 commits into
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Guard against running on an empty per-sample input list in tximport/quantify_rsem#12378pinin4fjords wants to merge 2 commits into
pinin4fjords wants to merge 2 commits into
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toSortedList() always emits (even []) on an empty upstream, unlike the collect() it replaced which emits nothing at all. Without a guard, that turns a channel that previously never triggered its downstream process into one that always does, running CUSTOM_RSEMMERGECOUNTS/TXIMETA_TXIMPORT once with zero staged files whenever no samples reach this point (e.g. all samples filtered out upstream). Filter to size() > 0 to restore the original no-op-on-empty behaviour.
pinin4fjords
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Jul 15, 2026
toSortedList() always emits (even []) on an empty upstream, unlike the collect() it replaced which emits nothing at all. Without a guard, a channel that previously never triggered its downstream process now always does, running CUSTOM_RSEMMERGECOUNTS/TXIMETA_TXIMPORT once with zero staged files whenever no samples reach this point (e.g. all samples filtered out upstream). Filter to size() > 0 to restore the original no-op-on-empty behaviour. Applied here ahead of the modules.json bump; nf-core/modules#12378 carries the same fix upstream. Once that merges, only the pinned git_sha needs updating.
jscgh
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Jul 16, 2026
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Description
Follow-up to #12377, caught by downstream CI on the nf-core/rnaseq consuming PR (nf-core/rnaseq#1885).
#12377swappedcollect()fortoSortedList()on the per-sample inputs feedingTXIMETA_TXIMPORTandCUSTOM_RSEMMERGECOUNTS, to make the staged input order (and therefore the task hash) deterministic. That swap has a side effect:toSortedList()always emits exactly one value, even[], on an empty upstream, whereas thecollect()it replaced emits nothing at all when the upstream is empty.In a pipeline run where every sample is filtered out before reaching this point (e.g. all samples fail a trim-length threshold), the per-sample channel closes with zero elements. With the old
collect(), that meantTXIMETA_TXIMPORT/CUSTOM_RSEMMERGECOUNTSwere never invoked at all - a queue channel with no matching emission on one side means no invocation. WithtoSortedList(), the channel now emits a single[]value, so the process fires once with zero staged files, producing empty output files instead of being skipped.Changes
Add
.filter { sorted -> sorted.size() > 0 }after eachtoSortedList()in both subworkflows, matching the guard already used forCUSTOM_TX2GENE's input in the same subworkflow. Restores the original no-op-on-empty behaviour while keeping the ordering deterministic for the non-empty case.PR checklist
nf-core subworkflows test quant_tximport_summarizedexperiment --profile dockerpasses, snapshot unchanged.nf-core subworkflows test quantify_rsem --profile dockerpasses, snapshot unchanged.