feat(gedi): add gedi/indexgenome and gedi/price modules#11693
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Adds two modules wrapping the GEDI / PRICE toolkit (`bioconda::gedi=1.0.6a`) for Ribo-seq translated-ORF discovery. PRICE (Erhard et al. 2018, doi:10.1038/nmeth.4631) calls translated ORFs from ribosome profiling data with near-cognate start codon detection. `gedi/indexgenome` wraps `gedi -e IndexGenome`, producing the `.oml` genome index directory consumed by PRICE. `gedi/price` wraps `bamlist2cit` + `gedi -e Price`, taking a cohort of Ribo-seq BAMs plus the genome index and emitting ORF predictions (`*.orfs.tsv` + `*.cit` + sidecars). One-shot across the cohort - PRICE is not per-sample. Both modules use Wave-built community containers from `bioconda::gedi=1.0.6a`. The bioconda recipe was merged 2026-05-16; using Wave directly for now. Source: nf-core/riboseq#174. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Previously hard-coded the output directory as `price_index`. Switching to
`${prefix}` (default `${meta.id}`, overridable via `task.ext.prefix`) lets
callers control the directory name and matches the nf-core convention for
publishable directory outputs.
The default ${meta.id} keeps the directory keyed to the reference id, so
when `gedi/price` opens `${index}/${meta2.id}.oml`, the lookup still
resolves provided meta ids match (already the case in the test chain).
Snapshot regenerated: the index directory name in the output snapshot
changes from `price_index` to the test's `homo_sapiens_chr20` (its meta.id).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2 tasks
Replaces the stub-only PRICE test with an end-to-end test that runs PRICE on a minimal cohort of four Ribo-seq samples (chr19+chr22, protein-coding-only reference). The cohort produces 380 ORF calls; snapshot captures the orfs.tsv line count for stability validation. Fixtures published in nf-core/test-datasets PR nf-core#2061. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…factor
The earlier `${prefix}` refactor (commit 0ca4c45) changed the index
output declaration from `path("price_index")` to `path("${prefix}")`,
but the meta.yml output entry still hard-coded `price_index` — causing
CI lint to flag `correct_meta_outputs: Module meta.yml does not match
main.nf`.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
… emit
After the `${prefix}` refactor (commit 0ca4c45) the index output line
was the only `tuple val(meta), path(...)` emit in the module, so the
52-space alignment padding it kept from when the path was `price_index`
no longer aligns with anything.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…dules into gedi-add-modules
Two cross-cutting fixes from review of nf-core#11693: - Licence was Apache-2.0 in both meta.yml files; the upstream repo erhard-lab/gedi is GPL-3.0. Corrected. - "GEDI (Gene Expression Data Integration)" was unverified — the upstream README/wiki/paper don't expand the acronym that way. Replaced with the upstream one-liner phrasing. PRICE meta.yml also adds the verified PRICE expansion (Probabilistic Inference of Codon Activities by an EM algorithm) from the GEDI wiki. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
nf-core/test-datasets#2061 merged; fixtures now live on the modules branch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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* feat(gedi): add gedi/indexgenome and gedi/price modules Adds two modules wrapping the GEDI / PRICE toolkit (`bioconda::gedi=1.0.6a`) for Ribo-seq translated-ORF discovery. PRICE (Erhard et al. 2018, doi:10.1038/nmeth.4631) calls translated ORFs from ribosome profiling data with near-cognate start codon detection. `gedi/indexgenome` wraps `gedi -e IndexGenome`, producing the `.oml` genome index directory consumed by PRICE. `gedi/price` wraps `bamlist2cit` + `gedi -e Price`, taking a cohort of Ribo-seq BAMs plus the genome index and emitting ORF predictions (`*.orfs.tsv` + `*.cit` + sidecars). One-shot across the cohort - PRICE is not per-sample. Both modules use Wave-built community containers from `bioconda::gedi=1.0.6a`. The bioconda recipe was merged 2026-05-16; using Wave directly for now. Source: nf-core/riboseq#174. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * refactor(gedi/indexgenome): use ${prefix} for the index output directory Previously hard-coded the output directory as `price_index`. Switching to `${prefix}` (default `${meta.id}`, overridable via `task.ext.prefix`) lets callers control the directory name and matches the nf-core convention for publishable directory outputs. The default ${meta.id} keeps the directory keyed to the reference id, so when `gedi/price` opens `${index}/${meta2.id}.oml`, the lookup still resolves provided meta ids match (already the case in the test chain). Snapshot regenerated: the index directory name in the output snapshot changes from `price_index` to the test's `homo_sapiens_chr20` (its meta.id). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(gedi/price): add real test using minimised chr19+chr22 fixtures Replaces the stub-only PRICE test with an end-to-end test that runs PRICE on a minimal cohort of four Ribo-seq samples (chr19+chr22, protein-coding-only reference). The cohort produces 380 ORF calls; snapshot captures the orfs.tsv line count for stability validation. Fixtures published in nf-core/test-datasets PR nf-core#2061. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(gedi/indexgenome): update meta.yml output name after ${prefix} refactor The earlier `${prefix}` refactor (commit 0ca4c45) changed the index output declaration from `path("price_index")` to `path("${prefix}")`, but the meta.yml output entry still hard-coded `price_index` — causing CI lint to flag `correct_meta_outputs: Module meta.yml does not match main.nf`. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * style(gedi/indexgenome): collapse leftover alignment padding on index emit After the `${prefix}` refactor (commit 0ca4c45) the index output line was the only `tuple val(meta), path(...)` emit in the module, so the 52-space alignment padding it kept from when the path was `price_index` no longer aligns with anything. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(gedi): correct licence (GPL-3.0) and Gedi description in meta.yml Two cross-cutting fixes from review of nf-core#11693: - Licence was Apache-2.0 in both meta.yml files; the upstream repo erhard-lab/gedi is GPL-3.0. Corrected. - "GEDI (Gene Expression Data Integration)" was unverified — the upstream README/wiki/paper don't expand the acronym that way. Replaced with the upstream one-liner phrasing. PRICE meta.yml also adds the verified PRICE expansion (Probabilistic Inference of Codon Activities by an EM algorithm) from the GEDI wiki. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(gedi/price): point fixtures at nf-core/test-datasets@modules nf-core/test-datasets#2061 merged; fixtures now live on the modules branch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Adds two new modules wrapping the GEDI / PRICE toolkit for Ribo-seq translated-ORF discovery (Erhard et al. 2018, doi:10.1038/nmeth.4631).
gedi/indexgenomeWraps
gedi -e IndexGenometo build the.omlGEDI genome index from a FASTA + GTF pair.tuple val(meta), path(fasta), path(gtf)tuple val(meta), path("${prefix}")(emit: index) — directory containing${meta.id}.oml+ sidecars; directory name defaults tometa.id, overridable viatask.ext.prefixtopic: versionsgedi/priceWraps
bamlist2cit+gedi -e Price. Takes a cohort of Ribo-seq BAMs plus the GEDI genome index and emits PRICE's ORF predictions. PRICE estimates a shared codon-position model across all input BAMs, so the cohort is processed as a single invocation (not per-sample).tuple val(meta), path(bams, stageAs: 'bams/*'), path(bais, stageAs: 'bams/*')— Ribo-seq cohorttuple val(meta2), path(index)— directory fromgedi/indexgenomeorfs_tsvplus optionalorfs_cit/orfs_metadata/codons_cit/model/signal/paramsidecars, andtopic: versionsContainers
Wave-built community containers backed by
bioconda::gedi=1.0.6a:community.wave.seqera.io/library/gedi_indexgenome:cfca16738f306c86community.wave.seqera.io/library/gedi_price:2392624d5f803049Test data
gedi/priceis exercised against a minimal Ribo-seq cohort (four samples, chr19+chr22, protein-coding-only reference) atdata/genomics/homo_sapiens/riboseq_expression/price/(added via nf-core/test-datasets#2061). Every fixture file < 4 MiB, ~11 MB total. PRICE produces 380 ORF calls; the test snapshot captures theorfs.tsvline count for stability.Test plan
nf-core modules test --profile docker gedi/indexgenome— green, two-pass stablenf-core modules test --profile docker gedi/price— green, two-pass stablenf-core modules lint --dir . gedi/{indexgenome,price}— 0 failures (warnings limited to Wave URL probe / tag-version cosmetic, same as other Wave-container modules)Source: nf-core/riboseq#174.