feat(ribocode,ribotish): pyfasta indexes, prefix-scoped outputs, optional ribotish -a

[pinin4fjords]

Bundles three in-place module changes carried in nf-core/riboseq#174. Each is self-contained and addresses a different pain point we hit running RiboCode / Ribo-TISH at scale.

ribocode/prepare

Pre-build the pyfasta .gdx/.flat indexes for annotation/transcripts_sequence.fa immediately after prepare_transcripts, using the same key_fn RiboCode applies internally (split on first space, otherwise split on |). The stub also touches the two new sidecars.

Why: downstream RiboCode steps open the FASTA with pyfasta, which lazily writes .gdx/.flat next to the input on first read. Under Fusion staging those writes land back at the upstream task's S3 prefix and silently corrupt the staged copy on retries. Building the indexes inside the producing task fixes it.

ribocode/ribocode

Switch the orf_txt and orf_txt_collapsed output globs from *.txt / *_collapsed.txt to ${prefix}.txt / ${prefix}_collapsed.txt so multi-instance publication is unambiguous (*.txt previously matched both the all-ORFs and collapsed files into the same emit). The prefix binding is promoted out of def in both script: and stub: so it resolves at the output-glob stage; the Nextflow 26 strict parser rejects re-declaring the same local with def across the two blocks.

The existing stub assertion that indexed process.out.orf_txt[0][1][0] is corrected to the new single-file shape (process.out.orf_txt[0][1]).

ribotish/predict

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.

Test plan

All three modules pass under Docker on a c5.9xlarge VM with nf-core 4.0.2 / nextflow 26.04.1 / nf-test 0.9.5:

nf-core modules test --profile docker ribocode/prepare
nf-core modules test --profile docker ribocode/ribocode
nf-core modules test --profile docker ribotish/predict

Snapshot deltas:

• ribocode/prepare: non-stub snapshot gains the two new file md5s (transcripts_sequence.fa.flat, transcripts_sequence.fa.gdx); existing files' md5s unchanged.
• ribocode/ribocode: orf_outputs snapshot drops the duplicate test_collapsed.txt entry that the old *.txt glob had pulled into orf_txt; everything else unchanged.
• ribotish/predict: no snapshot change (the [] migration is a no-op at runtime).

Source: nf-core/riboseq#174

[pinin4fjords]

Superseded by the per-module splits:

• ribocode (prepare + ribocode): feat(ribocode): pre-build pyfasta indexes + prefix-scoped outputs #11685
• ribotish/predict: feat(ribotish/predict): optional reference_gtf input + topics versions + 0.2.8 #11686

Closing this bundled draft. Branch ribocode-ribotish-bundled-fixes will be pruned once the splits land.