feat(ribotish/predict): optional reference_gtf input + topics versions + 0.2.8#11686
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feat(ribotish/predict): optional reference_gtf input + topics versions + 0.2.8#11686pinin4fjords wants to merge 2 commits into
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Carried in nf-core/riboseq#174 and split out of the bundled PR #11684. **Breaking signature change.** The third input tuple gains an optional fourth element, `reference_gtf`, plumbed through to `ribotish predict` as `-a <gtf>` when populated: tuple val(meta3), path(fasta), path(gtf), path(reference_gtf, stageAs: 'secondary.gtf') Callers must supply a fourth element on every emit. Pass `[]` for the no-op case (no secondary annotation). The existing test cases in this PR are migrated that way; positive-coverage tests for the populated path will land in a follow-up. Why: Ribo-TISH's `-a` argument is the documented hook for layering a secondary annotation (e.g. MANE/RefSeq) on top of the primary GTF, and we want to expose it from the module without a second optional input tuple. Source: nf-core/riboseq#174 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
… topics versions + bump 0.2.8 Three coupled cleanups in response to the lint feedback on PR #11686: 1. Move the new `reference_gtf` input out of the existing fasta/gtf tuple and into its own optional input tuple (meta7) - the convention this module already uses for `bam_ti`, `candidate_orfs`, `para_ribo`, and `para_ti`. The existing `(meta3, fasta, gtf)` signature is preserved, so callers no longer need to grow that tuple; they wire a separate `Channel.of([[], []])` (or a populated channel) into the new slot. 2. Migrate version reporting from the legacy `versions.yml` heredoc to the new topic-based emission (`tuple val("${task.process}"), val('ribotish'), eval('...'), topic: versions, emit: versions_ribotish`). The `versions.yml` heredoc is removed from both `script:` and `stub:`. `meta.yml` regenerated by `nf-core modules lint --fix` to add the `topics:` block and reshape the `versions_ribotish` output entry. 3. Bump ribotish from 0.2.7 to 0.2.8 (bioconda; build hash unchanged). Test snapshot regenerated under `--update`: versions snapshot key renamed from `versions_*` to `versions_ribotish_*`, version string updated to `0.2.8`. Prediction-table assertions unchanged - 0.2.8 is a patch release. Source: nf-core/riboseq#174 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
pinin4fjords
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Dear Claude, can you update the nf-test structure while you are at it, so that each test only has one snapshot (which doesn't need a name) |
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Adds an optional secondary GTF input to
ribotish predict(so callers can supply a MANE/RefSeq-style overlay via-awhile keeping the primary GTF on-g), and brings the module up to current nf-core conventions.Changes
tuple val(meta7), path(reference_gtf, stageAs: 'secondary.gtf'). When populated, plumbed through as-a <reference_gtf>on the ribotish command line. Lives in its own tuple - matches the pattern this module already uses forbam_ti,candidate_orfs,para_ribo,para_ti. Existing(meta3, fasta, gtf)signature is preserved, so consumers add a single new input channel rather than restructuring an existing tuple.path "versions.yml"emit +cat <<-END_VERSIONSheredoc replaced withtuple val("${task.process}"), val('ribotish'), eval("ribotish --version | sed 's/ribotish //'"), topic: versions, emit: versions_ribotish.meta.ymlregenerated vianf-core modules lint --fix(adds thetopics:block and reshapes theversions_ribotishoutput entry).environment.ymlupdated).Test plan
nf-core modules test --profile docker ribotish/predictruns all four cases green (single/multi ribo bam × main/stub). Snapshot regenerated:versions_*keys renamed toversions_ribotish_*(matching the new emit name).0.2.7→0.2.8.Caller migration
Existing callers must add a 7th input slot. Pass
Channel.of([[], []])(or[[id:'reference'], []]) for the no-op case; pass a populated[meta, gtf_path]to use-a.Source: nf-core/riboseq#174. Supersedes the ribotish half of #11684.