fix(orftable_fasta_gtf_buildorfcatalogue): keep meta.id as the true sample id - #12896
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pinin4fjords merged 5 commits intoSep 8, 2026
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Missed pushing this from the VM verification run earlier - the code fix was correct but the committed snapshot still had the old (sample1.ribotish/sample1.ribocode) sample_id content hash.
luisas
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Sep 8, 2026
ext.prefix/ext.args config closures see every declared process input by name, not just meta - confirmed empirically. No need to duplicate caller into meta just to reach it from config.
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…orfcatalogue Drop meta.caller, reference caller directly in ext.prefix - config closures see every declared process input by name, not just meta. Matches nf-core/modules#12896 after reviewer feedback. Output is byte-identical, no snapshot changes needed.
pinin4fjords
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…mits fastq_qc_trim_filter_setstrandedness -> 0853b48c (nf-core/modules#12895) orftable_fasta_gtf_buildorfcatalogue -> 7baf88e0 (nf-core/modules#12896) Both PRs are merged. Synced modules.json and the two changed files to their exact merge-commit content (not current master HEAD, to avoid pulling in unrelated later changes). orftable_fasta_gtf_buildorfcatalogue was already byte-identical (riboseq's copy already matched). Resolves the check_local_copy lint failures that were expected pending these merges.
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Summary
ORFTABLE_FASTA_GTF_BUILDORFCATALOGUEdisambiguatesCUSTOM_ORFNORMALISE's output filenames per caller by appending the caller name tometa.id("${meta.id}.${caller}") before calling the module. ButCUSTOM_ORFNORMALISEwritesmeta.idstraight through into each row'ssample_idcolumn, andCUSTOM_ORFMERGE's consensus view counts distinctsample_ids forn_samples/--min-samplesfiltering. So an ORF called by two different callers on the same sample gets counted as two samples, not one — corrupting the publishedn_samples/samplescatalogue columns, and the--min-samplesconsensus filter for anyone raising it above the default of 1.The subworkflow's own doc comment already states the intended contract ("caller id carried as a per-record val (not in meta)") — the code just didn't follow it.
What changed
ch_normalise_innow setsmeta.callerinstead of mutatingmeta.id.ext.prefixoverride in this subworkflow's ownnextflow.config("${meta.id}.${meta.caller}.normalised") to keep output filenames byte-identical to before, following the exact convention already established incustom/orfmerge's own test fixture (tests/setup_prefix.config).No test changes needed — the existing
ribotish + ribocodetest already exercises two callers on the same sample id (sample1), and its snapshot now correctly showssample_id = sample1(wassample1.ribotish/sample1.ribocode).Found while reviewing nf-core/riboseq's v2.0.0 release PR, which vendors this subworkflow.