Search results

feat(ribotish/predict): wire optional -a reference annotation through pipeline

Status: Open.

#179 In nf-core/riboseq;

· pinin4fjords opened on May 22, 2026

STAR alignment params: consider Ribo-seq-tuned defaults per sample type

Status: Open.

#173 In nf-core/riboseq;

· pinin4fjords opened on May 17, 2026

feat: second STAR pass against hybrid transcriptome to give RiboCode equal novel-locus coverage

enhancementNew feature or requestNew feature or request

Status: Open.

#171 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: add PRICE as Tier-2 opt-in for near-cognate ORF discovery

enhancementNew feature or requestNew feature or request

Status: Open.

#170 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: add Rp-Bp as Tier-1 ORF caller (opt-in, overnight mode)

enhancementNew feature or requestNew feature or request

Status: Open.

#169 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: ORF-level differential translation analysis (DT, DTE, and DOU)

enhancementNew feature or requestNew feature or request

Status: Open.

#168 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: cross-sample ORF catalogue — merge, deduplicate, and re-quantify across all samples

enhancementNew feature or requestNew feature or request

Status: Open.

#167 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: ORF-level P-site quantification — replace gene-level counting with per-ORF counts

enhancementNew feature or requestNew feature or request

Status: Open.

#166 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: wire hybrid GTF (canonical + novel intergenic) into ORF callers

enhancementNew feature or requestNew feature or request

Status: Open.

#165 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

feat: StringTie novel transcript discovery — RNA-seq BAMs preferred, user-supplied GTF bypass, intergenic-only filter

enhancementNew feature or requestNew feature or request

Status: Open.

#164 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

fix: demote Ribotricer to opt-in ORF caller

bugSomething isn't workingSomething isn't working

Status: Open.

#163 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026

investigate: confirm correct GTF input for ribotish quality in hybrid annotation mode

questionFurther information is requestedFurther information is requested

Status: Open.

#162 In nf-core/riboseq;

· pinin4fjords opened on May 14, 2026