feat(ribotish/predict): expose optional secondary annotation GTF input (-a flag)

[pinin4fjords]

Summary

ribotish predict accepts a -a flag for a secondary annotation file, used for ORF background modelling and TisType classification independently of the primary discovery target (-g). The current nf-core module exposes only a single GTF input. This PR adds the optional second input.

Use case: when the nf-core/riboseq pipeline discovers ORFs on novel StringTie transcripts (no CDS), passing the canonical annotation separately via -a allows Ribo-TISH to correctly classify ORF types (Novel, CDSFrameOverlap, 5utr, etc.) and model translation background against known coding sequences, while scanning only the novel transcripts for new calls.

Change

input:
    tuple val(meta), path(bam), path(bai)
    path(gtf)                // -g: discovery target
    path(reference_gtf)      // -a: optional; secondary annotation for classification

Script block:

def secondary_gtf = reference_gtf.name != 'NO_FILE' ? "-a ${reference_gtf}" : ""

ribotish predict \
    ${args} \
    -b ${bam} \
    -g ${gtf} \
    ${secondary_gtf} \
    ...

Declare reference_gtf as optional (use path(reference_gtf, stageAs: 'NO_FILE', optional: true) or equivalent) so existing callers passing a single GTF continue to work without modification.

References

• Ribo-TISH README (-a flag): https://github.com/zhpn1024/ribotish
• Zhang et al. (2017) Nat Commun. DOI: 10.1038/s41467-017-01981-8
• Current module: modules/nf-core/ribotish/predict

Required by: nf-core/riboseq novel ORF discovery wiring (companion pipeline issue: nf-core/riboseq#163)