docs(orfnormalise): correct the GTF contract for rpbp and price - #12453
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docs(orfnormalise): correct the GTF contract for rpbp and price#12453pinin4fjords wants to merge 2 commits into
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Both resolve gene_id from the ORF's transcript id through the supplied annotation, so the GTF is not unused for them and an empty one is not acceptable: price falls back to its Gene column, which concatenates every gene the ORF's genomic span overlaps. State the requirement that the annotation be a superset of what each caller was run against, in the module and in the orftable_fasta_gtf_buildorfcatalogue subworkflow that passes it through.
mashehu
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Jul 28, 2026
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since it's docs only, can you please try to write them in your own words?
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| Annotation GTF. Every caller draws on it: ribocode requires it | ||
| (transcript-relative coordinates → genomic lift), ribotish and | ||
| ribotricer use it for multi-exon block recovery (from GenomePos | ||
| and the ORF_ID span respectively), and rpbp and price resolve | ||
| `gene_id` from the ORF's transcript id through it. Supply the | ||
| annotation the caller was run against, or a superset of it: a | ||
| transcript missing here cannot be resolved, and price then falls | ||
| back to its `Gene` column, which concatenates every gene the | ||
| ORF's genomic span overlaps. Passing `[ [:], [] ]` loses | ||
| multi-exon structure and, for rpbp and price, `gene_id`. |
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can you please rewrite this in your own words, feels like marketing speak
pinin4fjords
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July 28, 2026 14:37
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Doc-only.
custom/orfnormalise'sgtfinput is documented as unused forrpbpandprice, with[ [:], [] ]offered as acceptable when the caller subset excludesribocodeandribotish. Neither holds:parse_rpbpresolvesgene_idastranscripts[tid].gene_id, so with no GTF every rpbp row gets an emptygene_id.parse_priceresolvesgene_idfrom the transcript id in theIdcolumn (fix(custom/orfnormalise): resolve PRICE gene ids from the annotation #12436), falling back to PRICE'sGenecolumn, which concatenates every gene the ORF's genomic span overlaps. With no GTF, every price row degrades to that compound value, which joins against nothing downstream.There is also an unstated requirement worth writing down: the annotation has to be a superset of the one each caller was run against. A transcript absent from it cannot be resolved, and a pipeline that hands the normaliser a narrower annotation than its callers used (a one-transcript-per-gene backbone, say) silently loses gene ids for ORFs on the isoforms it dropped.
Corrected in the module's
meta.ymland in theorftable_fasta_gtf_buildorfcataloguesubworkflow that passes the GTF through (meta.ymland thetake:comment), which carried the same claim.No behaviour change.
nf-core modules lint custom/orfnormaliseandnf-core subworkflows lint orftable_fasta_gtf_buildorfcataloguepass (the two module warnings are pre-existing container-version notes).🤖 Generated with Claude Code