feat: Rp-Bp opt-in ORF caller#186
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Add Rp-Bp (Malone et al. 2017) as an opt-in ORF caller via --run_rpbp (default false). Implemented via the upstream fasta_gtf_bam_rpbp subworkflow (nf-core/modules#11695): six per-tool processes (extract-metagene-profiles, estimate-metagene-profile-bayes-factors, select-periodic-offsets, extract-orf-profiles, estimate-orf-bayes-factors, select-final-prediction-set) plus a shared prepare-genome. Honours --extended_orf_analysis: the upstream subworkflow takes the hybrid GTF when extended-ORF mode is active. New params: --run_rpbp --extra_rpbp_preparegenome_args --extra_rpbp_predictorfs_args Per-sample predicted-ORF BED + DNA + protein FASTA under <outdir>/orf_predictions/rpbp/. Stan MCMC fit takes ~20-24h per replicate at genome-wide scale; pipeline emits a runtime warning when enabled. modules.json currently pins rpbp modules + fasta_gtf_bam_rpbp subworkflow to nf-core/modules#11695 (branch rpbp-add-modules-and-subworkflows, sha c07e919d). Once #11695 merges, run nf-core modules update + nf-core subworkflows update to swap the 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. |
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Reconcile the Rp-Bp slice onto the post-#185 dev tree: relocate Rp-Bp from the pre-refactor inline workflow form into orf_caller_dispatch (gated on --run_rpbp), take the upstream rpbp modules and fasta_gtf_bam_rpbp subworkflow at their merged-to-master pins, and land the --run_rpbp wiring, config, schema, docs and changelog entry. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Rp-Bp builds its candidate ORF set per transcript isoform and deduplicates by genomic coordinates, then resolves overlaps itself (longest-per-stop, best Bayes factor). Feeding it the one-transcript-per-gene canonical backbone silently dropped isoform-specific ORFs (alt-5'UTR uORFs, N-terminal extensions/truncations, retained-intron/alt-exon ORFs) and biased ORF-type labelling toward canonical CDS, with no compensating benefit. Route it to the full ch_gtf (default) like PRICE; extended mode keeps the hybrid GTF for novel transcripts. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…annotation Document, in the Rp-Bp and PRICE usage sections, that both callers receive the full --gtf rather than the canonical one-transcript-per-gene backbone: each enumerates/handles ORFs across all isoforms and resolves overlaps itself, so collapsing to canonical would drop isoform-specific ORFs and bias ORF-type labels. Cites Malone et al. 2017. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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suhrig
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Jun 25, 2026
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Thanks @suhrig ! |
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Summary
Adds Rp-Bp (Malone et al. 2017) as an opt-in ORF caller via
--run_rpbp(defaultfalse), wired into theorf_caller_dispatchsubworkflow through the upstreamfasta_gtf_bam_rpbpnf-core subworkflow (8 modules: seven per-tool steps plus a sharedprepare-genome). The pipeline's standard STAR alignment is reused rather than re-running Rp-Bp's own alignment, and each step caches independently on resume.Changes
rpbp/*modules (8) + thefasta_gtf_bam_rpbpsubworkflow.--run_rpbp,--extra_rpbp_preparegenome_args,--extra_rpbp_predictorfs_args.orf_caller_dispatchgains a--run_rpbp-gated Rp-Bp block;rpbpjoins the runtime-enabled caller set and (unlike Ribotricer) its Bayes-factor score is retained in cross-caller rank aggregation.--extended_orf_analysis(hybrid GTF when active).conf/modules.config: time budget on the Bayesian-fit modules, final-prediction-set filtering args, publish to<outdir>/orf_predictions/rpbp/.Annotation: full multi-isoform GTF
Rp-Bp is given the full
--gtfannotation, not the one-transcript-per-gene canonical backbone (mirroring PRICE). Rp-Bp enumerates candidate ORFs across every transcript isoform and resolves redundant/overlapping ORFs itself (longest-per-stop, best Bayes factor), so collapsing to canonical would silently drop ORFs that exist only on non-canonical isoforms (alternative-5'UTR uORFs, isoform-specific N-terminal extensions/truncations, retained-intron and alternative-exon ORFs) and bias the reported ORF types toward canonical CDS, with no compensating benefit. Rationale and citations are in the Rp-Bp section ofdocs/usage.md(Malone et al. 2017, NAR). Under--extended_orf_analysisRp-Bp instead takes the hybrid GTF so novel transcripts are within discovery scope.Caveats
src/rpbp/defaults.py): most notably STAR-default mismatch filtering (outFilterMismatchNmax 10/outFilterMismatchNoverLmax 0.3, vs rp-bp's1/0.04), and the absence ofoutFilterType BySJout,outFilterIntronMotifs RemoveNoncanonicalUnannotated,seedSearchStartLmaxOverLread 0.5andwinAnchorMultimapNmax 100. This affects every genome-BAM ORF caller, not just Rp-Bp. We will address this in #173 by applying Ribo-seq-tuned STAR parameters per sample type (tightened for Ribo-seq, unchanged for RNA-seq); in the meantime--extra_star_align_argslets you opt in for Ribo-seq-only runs. Rp-Bp processes whatever alignments it is given, so this shifts which footprints are counted rather than being a correctness issue. Seedocs/usage.mdfor the full parameter list and override hint.Part of the #174 modernisation stack.
Closes #169
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