feat: ORF-level differential translation#189
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(Tier 1) Gene-level TE numerator re-aggregation: ORF_TO_GENE_CDS_COUNTS sums ONLY canonical_cds ORFs from the catalogue (via orf_to_gene.tsv + catalogue_tsv classification) back to gene level, replacing the plastid-derived gene-CDS counts before REPLACE_RIBOSEQ_COUNTS_IN_MATRIX. Keeps the gene-level TE clean of uORF / dORF dynamics. (Tier 2) Per-ORF DTE: DTE_COUNTS_PREP joins per-ORF Ribo-seq P-site counts with gene-level Salmon RNA-seq counts via orf_to_gene.tsv. Feeds the existing DESEQ2_DELTATE / ANOTA2SEQ_ANOTA2SEQRUN engines (aliased) at ORF resolution. Gated on --extended_orf_analysis + catalogue exists + --skip_plastid false. Adds --run_dotseq placeholder (no-op until #11742 lands). Row-independence caveat: ORFs sharing a gene-level Salmon denominator are perfectly correlated after the join.
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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. |
… failing The previous strict-overlap check rejected the common riboseq wiring, where the secondary matrix is Salmon's gene-level all-sample quant fed in for its RNA-seq columns but still carries the Ribo-seq columns alongside. Primary's columns are authoritative for the primary role, so drop the overlap from secondary and log it to stderr rather than hard-erroring at runtime. A degenerate-case guard remains: if secondary has zero columns left after the drop, the script exits with a clear "no role-specific samples left" message. This unblocks the existing novel_gtf and stringtie_extended tests (which were failing on 25.04.8 CI at DTE_COUNTS_PREP (allsamples)) as well as the ORF-level dotseq / deltate / anota2seq paths. [skip ci] Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
Wire DOTSEQ_DOTSEQ_ORF through DTE_COUNTS_PREP at ORF resolution. Drop the --run_dotseq placeholder; dotseq is now a third value for --translational_efficiency_method. Module installed from nf-core/modules#11742-pending (registered under https://github.com/pinin4fjords/nf-core-modules.git so nf-core lint doesn't hit an interactive prompt under CI's no-TTY shell). Adds withName blocks for the ORF-level DTE chain plus extra_orf_dte_args / extra_dotseq_args params, and brings tests/dotseq.nf.test + snapshot. [skip ci]
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Summary
Closes the modernisation arc on differential translation by adding two complementary paths:
ORF_TO_GENE_CDS_COUNTSsums onlycanonical_cds-class ORFs from the catalogue back to gene level (viaorf_to_gene.tsv+catalogue_tsv), replacing the plastid-derived gene-CDS Ribo-seq counts beforeREPLACE_RIBOSEQ_COUNTS_IN_MATRIX. Keeps the gene-level TE numerator clean of uORF / dORF dynamics.DTE_COUNTS_PREPjoins the per-ORF Ribo-seq P-site counts (feat: ORF-level P-site quantification — replace gene-level counting with per-ORF counts #166) with the gene-level Salmon RNA-seq counts viaorf_to_gene.tsv(novel intergenic ORFs without a host gene drop out). The matrix feeds the existingDESEQ2_DELTATE/ANOTA2SEQ_ANOTA2SEQRUNengines (aliased as*_ORF) at ORF resolution.Changes
orf_to_gene_cds_counts,dte_counts_prep.--extended_orf_analysis true+ catalogue exists +--skip_plastid false.--run_dotseq(placeholder; no-op until Add dotseq/dotseq modules#11742 lands the DOTSeq module).Row-independence caveat
The per-ORF DTE path joins Ribo-seq ORF counts to a gene-level RNA-seq denominator. ORFs sharing a gene-level denominator are perfectly correlated after the join, so per-ORF test statistics underestimate uncertainty for sibling ORFs. Treat the per-ORF p-values as exploratory; the gene-level TE (Tier 1, with canonical-CDS-only aggregation) is the inference-grade output.
What's deferred
FILTER_COUNTS_CANONICAL(restrict gene-level DTE to canonical gene IDs) is on aggregation but layered in later; if you want it here, follow-up commit.Stacked PR notes
Thirteenth and final in the stack splitting #174. Targets #188 (
feat/166-orf-quantification).Closes #168
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