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feat(ribotish/predict): wire optional -a reference annotation through pipeline Fix linting from a comment #91: Issue comment #179 (comment) created by pinin4fjords
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feat: second STAR pass against hybrid transcriptome to give RiboCode equal novel-locus coverage Fix linting from a comment #90: Issue comment #171 (comment) created by pinin4fjords
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feat: add PRICE as Tier-2 opt-in for near-cognate ORF discovery Fix linting from a comment #89: Issue comment #170 (comment) created by pinin4fjords
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feat: add Rp-Bp as Tier-1 ORF caller (opt-in, overnight mode) Fix linting from a comment #88: Issue comment #169 (comment) created by pinin4fjords
Skipped
Skipped
feat: ORF-level differential translation analysis (DT, DTE, and DOU) Fix linting from a comment #87: Issue comment #168 (comment) created by pinin4fjords
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feat: cross-sample ORF catalogue — merge, deduplicate, and re-quantify across all samples Fix linting from a comment #86: Issue comment #167 (comment) created by pinin4fjords
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feat: ORF-level P-site quantification — replace gene-level counting with per-ORF counts Fix linting from a comment #85: Issue comment #166 (comment) created by pinin4fjords
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feat: wire hybrid GTF (canonical + novel intergenic) into ORF callers Fix linting from a comment #84: Issue comment #165 (comment) created by pinin4fjords
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feat: StringTie novel transcript discovery — RNA-seq BAMs preferred, user-supplied GTF bypass, intergenic-only filter Fix linting from a comment #83: Issue comment #164 (comment) created by pinin4fjords
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fix: demote Ribotricer to opt-in ORF caller Fix linting from a comment #82: Issue comment #163 (comment) created by pinin4fjords
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investigate: confirm correct GTF input for ribotish quality in hybrid annotation mode Fix linting from a comment #81: Issue comment #162 (comment) created by pinin4fjords
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feat: support one-transcript-per-gene canonical annotation backbone (MANE Select / Ensembl canonical) Fix linting from a comment #80: Issue comment #161 (comment) created by pinin4fjords
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fix: make plastid_psite the default --te_quantification_method Fix linting from a comment #79: Issue comment #160 (comment) created by pinin4fjords
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Port StringTie-based novel transcript discovery from nf-core/rnaseq Fix linting from a comment #78: Issue comment #157 (comment) created by pinin4fjords
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Important! Template update for nf-core/tools v4.0.2 nf-core AWS full size tests #157: Pull request #156 submitted by pinin4fjords
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nf-core linting comment nf-core linting comment #2212: completed by pinin4fjords
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nf-core linting comment nf-core linting comment #2211: in_progress by pinin4fjords
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nf-core linting comment nf-core linting comment #2210: requested by pinin4fjords
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Important! Template update for nf-core/tools v4.0.2 Run nf-test #361: Pull request #156 synchronize by pinin4fjords
35m 49s nf-core-template-merge-4.0.2
nf-core-template-merge-4.0.2
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Important! Template update for nf-core/tools v4.0.2 nf-core linting #730: Pull request #156 synchronize by pinin4fjords
3m 7s nf-core-template-merge-4.0.2
nf-core-template-merge-4.0.2
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Important! Template update for nf-core/tools v4.0.2 nf-core template version comment #493: Pull request #156 synchronize by pinin4fjords
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Important! Template update for nf-core/tools v4.0.2 nf-core template version comment #492: Pull request #156 synchronize by pinin4fjords
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chore: update all modules and subworkflows to latest nf-core AWS full size tests #156: Pull request #194 submitted by pinin4fjords
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chore: update all modules and subworkflows to latest nf-core AWS full size tests #155: Pull request #194 submitted by luisas
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Close user-tagged issues and PRs Close user-tagged issues and PRs #72: Scheduled
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master
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