nf-core/rnaseq: nf-core/rnaseq v3.25.0 - Plutonium Pangolin

What's Changed

• Bump version to 3.25.0dev; fix SortMeRNA sample name in MultiQC by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1781
• refactor: delocalise GTF_FILTER to nf-core custom/gtffilter by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1782
• fix: wire up skip_gtf_transcript_filter to CUSTOM_GTFFILTER ext.args by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1783
• Replace local gtf2bed with nf-core ea-utils/gtf2bed module by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1784
• refactor: replace local BAM QC with nf-core bam_qc_rnaseq subworkflow by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1786
• feat: add GPU support for ribodetector by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1790
• refactor: centralize module configs in conf/modules/ by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1788
• Bump custom/multiqccustombiotype to fail loudly on high biotype cardinality by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1795
• feat: add strand-agnostic bigwig, skip per-strand for unstranded libraries by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1792
• Fix MultiQC collapsing _1/_2 sample IDs via per-sample lookbehind by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1793
• docs: clarify prokaryotic transcript extraction includes tRNA/rRNA/tmRNA/ncRNA by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1796
• Add stringtie_merge for de novo assembly by @Odulhin in https://github.com/nf-core/rnaseq/pull/1755
• fix(prokaryotic): skip StringTie by default in the prokaryotic profile by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1804
• fix: per-sample MultiQC progressive closure via structural .join chain by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1803
• feat(bowtie2_salmon): report up to -k 200 alignments so Salmon EM can work by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1806
• fix(sortmerna): adopt SortMeRNA SILVA 138 smr_v4.3_default_db as the default rRNA database by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1811
• fix(mqc): strandedness table rows reflect which analyses ran; narrow prokaryotic RSeQC skip by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1805
• test: dedupe pipeline-level tests without losing coverage by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1812
• chore: sync nf-core components and retire ch_versions plumbing by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1814
• test(cleanup): gate pipeline-test cleanup on CI to keep local reruns stable by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1815
• Bump version to 3.25.0 ahead of release by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1799
• fix(prokaryotic): derive gene BED via gffread --bed by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1817
• chore: drop redundant versions.yml filters from saveAs closures by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1818
• fix(prokaryotic): skip RSeQC infer_experiment on bowtie2_salmon + skip sentieon on conda by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1819
• Dev -> master for nf-core/rnaseq 3.25.0 by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1816

New Contributors

• @Odulhin made their first contribution in https://github.com/nf-core/rnaseq/pull/1755

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.24.0...3.25.0