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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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. |
Rebuild the cross-sample ORF catalogue slice on the reconciled dev base (ORF_CALLER_DISPATCH structure). The catalogue's per-caller prediction channels now come from ORF_CALLER_DISPATCH.out.* rather than the inline caller blocks of the original branch base. Catalogue components taken from the upstream-pinned form: custom/orfnormalise, custom/orfmerge, custom/orfcollapse, mmseqs/easycluster, bedtools/getfasta, seqkit/translate and the orftable_fasta_gtf_buildorfcatalogue subworkflow, all pinned to nf-core/modules master. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
custom/orfmerge gains --min-callers / --min-samples (default 1, no
filtering) and emits an additional consensus catalogue view
(*.consensus.{bed12,tsv,orf_to_gene.tsv}) restricted to ORFs supported by
at least that many distinct callers and recurring in at least that many
samples. The full unfiltered catalogue is still published as before; the
consensus view is published under <outdir>/orf_catalogue/consensus/.
Surfaced via --orf_min_callers / --orf_min_samples; 2+ gives a consensus
catalogue that tames downstream ORF-level multiple testing.
The peptide-level smORF collapse is now behind --skip_orf_collapse
(default off, so collapse runs as before), wired to the catalogue
subworkflow's val_collapse argument.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The smORF-only restriction and locus-agnostic amino-acid clustering are this pipeline's design choices, not properties of the GENCODE Ribo-seq ORF consolidation. MMseqs2 global identity (--min-seq-id 0.9) approximates rather than reproduces GENCODE's longest-shared-substring / P-site-overlap collapse_cutoff 0.9. Docstring reworded to state both departures explicitly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add a --min-samples 2 case asserting the consensus catalogue is a non-empty strict subset of the full catalogue and every retained ORF meets the recurrence threshold, while the full catalogue is unchanged. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
novel_gtf and stringtie_extended now produce the cross-sample ORF catalogue (orf_catalogue/, including the consensus/ view and the normalised/ per-caller inputs) under --extended_orf_analysis true. Regenerated on x86_64 (NXF 25.04.8, nf-test 0.9.3, --profile=+docker). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…onsensus-view code [skip ci] Match the vendored orfmerge template (two-pass catalogue write), its regenerated module snapshot, and the orftable subworkflow (consensus emits + regenerated snapshot) to the upstream nf-core/modules implementation, so the eventual re-pin is a modules.json sha bump with no file changes. Output is byte-identical, so the pipeline snapshots are unaffected. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…th upstream [skip ci] Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Sync custom/orfcollapse + the orftable subworkflow to the upstream consensus-after-collapse implementation, and route the published orf_catalogue/consensus/ from CUSTOM_ORFCOLLAPSE (the de-redundified catalogue) when collapse runs, falling back to CUSTOM_ORFMERGE when --skip_orf_collapse is set. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…s #12167 merge custom/orfmerge, custom/orfcollapse and the orftable_fasta_gtf_buildorfcatalogue subworkflow now match their pinned sha (76e959312e), clearing the module_changes divergence carried while #12167 was in review. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
suhrig
approved these changes
Jun 26, 2026
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Summary
Builds a cohort-level cross-caller ORF catalogue under$\leq$ 100 aa), recording cross-caller (
--extended_orf_analysis true. Each enabled caller's per-sample output (Ribo-TISH, RiboCode, Ribotricer, Rp-Bp, PRICE) is normalised to a unified BED12 + sidecar TSV, then merged class-aware (transcript-ID grouping for annotated multi-exon CDS; 80% reciprocal overlap for single-exon novel intergenic and smORFscalled_by_*/score_*) and cross-sample (n_samples) evidence per ORF.smORFs are then peptide-level deduplicated with MMseqs2 (
--min-seq-id 0.9 -c 0.8), folding micropeptides encoded at multiple loci down to one representative (GENCODE Ribo-seq ORF catalogue convention, Mudge et al. 2022); opt out with--skip_orf_collapse.Outputs land under
<outdir>/orf_catalogue/:*.catalogue.{bed12,tsv,orf_to_gene.tsv,fasta}plus a MultiQC custom-content per-class count table.Consensus view
A consensus view is published under
<outdir>/orf_catalogue/consensus/, filtered to ORFs supported by at least--orf_min_callersdistinct callers and recurring in at least--orf_min_samplessamples (both default1, i.e. no filtering, so it equals the full catalogue out of the box). The filter runs after the smORF collapse, so it is the high-confidence subset of the de-redundified catalogue and a micropeptide folded across loci is judged on its combined cross-caller / cross-sample evidence. The full unfiltered catalogue is always published regardless; raising either threshold (e.g.--orf_min_callers 2) gives a consensus catalogue that tames downstream ORF-level multiple testing.Components
Built from upstream nf-core/modules components (all pinned to
master): theorftable_fasta_gtf_buildorfcataloguesubworkflow pluscustom/orfnormalise,custom/orfmerge,custom/orfcollapse,mmseqs/easycluster,bedtools/getfastaandseqkit/translate.The catalogue runs once per pipeline invocation, gated on
--extended_orf_analysis trueand a non-empty enabled-caller set; the default-off path is unchanged.Closes #167
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