feat: cross-sample ORF catalogue#187
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Gather per-sample, per-caller ORF predictions (Ribo-TISH, RiboCode,
Ribotricer, Rp-Bp, PRICE), normalise each to a unified BED12 + sidecar
TSV, then merge into a cohort-level catalogue with a class-aware
strategy (transcript-ID grouping for annotated multi-exon CDS, 80%
reciprocal overlap for single-exon novel intergenic and smORFs).
Emits orf_catalogue.{bed12,tsv}, orf_to_gene.tsv, and an AA FASTA
under <outdir>/orf_catalogue/, plus a MultiQC custom-content per-class
count table.
Implementation uses the upstream orftable_fasta_gtf_buildorfcatalogue
subworkflow (nf-core/modules#11740): CUSTOM_ORFNORMALISE per caller,
CUSTOM_ORFMERGE for cohort-level merge, BEDTOOLS_GETFASTA +
SEQKIT_TRANSLATE to produce the catalogue AA FASTA.
Per-caller prediction channels (ch_*_predictions) default to
Channel.empty() and are overridden inside each caller's if-block,
gating the catalogue invocation on extended_orf_active +
at-least-one-caller.
modules.json currently pins custom/orfnormalise, custom/orfmerge,
and the orftable_fasta_gtf_buildorfcatalogue subworkflow to
nf-core/modules#11740 (branch custom-orf-catalogue, sha 6597190c).
Once #11740 merges, run nf-core modules update / subworkflows update
to swap pins to master.
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Summary
Builds a cohort-level ORF catalogue across all enabled callers (Ribo-TISH, RiboCode, Ribotricer, Rp-Bp, PRICE) by normalising each per-sample output to a unified BED12 + sidecar TSV, then merging with a class-aware collapse:
Emits
orf_catalogue.{bed12,tsv},orf_to_gene.tsv, and an AA FASTA under<outdir>/orf_catalogue/, plus a MultiQC custom-content per-class count table.Changes
orftable_fasta_gtf_buildorfcatalogue(feat(custom): orfnormalise + orfmerge modules + orftable_fasta_gtf_buildorfcatalogue subworkflow modules#11740) and its module dependencies (custom/orfnormalise,custom/orfmerge,bedtools/getfasta,seqkit/translate).ch_ribotish_predictions,ch_ribocode_predictions,ch_ribotricer_predictions,ch_rpbp_predictions,ch_price_predictions) default toChannel.empty()and are overridden inside each caller's if-block.--extended_orf_analysis trueand at least one ORF caller enabled.withNameblocks for the three subworkflow processes, publishing under<outdir>/orf_catalogue/.🚨 Upstream dependency (blocker)
Depends on nf-core/modules#11740 (
feat(custom): orfnormalise + orfmerge modules + orftable_fasta_gtf_buildorfcatalogue subworkflow), currently OPEN.modules.jsonis pinned to the PR branch SHA. Before this PR can leave draft:master.nf-core modules install custom/orfnormalise custom/orfmergeandnf-core subworkflows install orftable_fasta_gtf_buildorfcataloguesomodules.jsonshows the master SHA.Stacked PR notes
Eleventh in the stack splitting #174. Targets #186 (
feat/169-rpbp).Closes #167
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