fix: EPICORE runs only once when --fasta is used#446
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ch_fasta is a queue channel with one item when --fasta is set. Paired positionally with SUMMARIZE_RESULTS.out.epicore_input (N items), EPICORE runs only once instead of per sample. Convert ch_fasta to a value channel with .first() so it broadcasts. Symptom: with --epicore, only one results/<sample>.tsv file is produced regardless of sample count.
axelwalter
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jonasscheid and
marissaDubbelaar
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Just confirmed the fix works as intended. |
jonasscheid
approved these changes
Apr 22, 2026
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Symptom
When running the pipeline with
--epicoreand--fasta <file>, only oneresults/<sample>.tsvfile is produced, regardless of how many samples were processed. For an N-sample run, only the first sample to reachSUMMARIZE_RESULTSgets an EPICORE output; the rest are silently dropped. No error is raised.Confirmed on a user run: 14
SUMMARIZE_RESULTStasks completed, but only 1EPICOREtask was ever submitted.Root cause
In
subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf(~line 139), when--fastais set,ch_fastais built withchannel.fromPath(params.fasta, ...)— a queue channel carrying a single item, not a value channel.In
workflows/mhcquant.nf:207, that one-item queue channel is paired withSUMMARIZE_RESULTS.out.epicore_input(an N-item queue channel, one item per sample/condition group). Nextflow pairs queue-to-queue positionally: the fasta channel drains after the first iteration and the remaining N-1epicore_inputitems never trigger anEPICOREtask.Because
conf/modules.configsetsSUMMARIZE_RESULTS.publishDir.enabled = !params.epicore, EPICORE's TSV is what the user sees inresults/when--epicoreis on — so the missing runs translate directly into missing output files.Introduced in the
fix/summarize-result-quantmerge (#444, commitb046949), which first wiredEPICOREin with this call signature.Fix
One character —
.first()converts the single-item queue channel into a value channel, which broadcasts to every matching item in the other channel:Behavior
--fasta --epicore: now produces oneresults/<sample>.tsvper sample (previously one total).--fasta): unchanged — this code path constructsch_fastadifferently and is not affected by this fix.Files changed
workflows/mhcquant.nf— one-character fix on line 207CHANGELOG.md—### Fixedentry under3.2.0dev