Dev -> master for nf-core/rnaseq 3.25.0

.github/workflows/nf-test-arm.yml

@@ -51,8 +51,8 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
           # Skip sentieon tests - no ARM containers available
           SKIP_SENTIEON: true
-          # Skip parabricks tests - requires NVIDIA GPU
-          SKIP_PARABRICKS: true
+          # Skip GPU tests - requires NVIDIA GPU
+          SKIP_GPU: true
         with:
           max_shards: 14
 
@@ -103,8 +103,8 @@ jobs:
           NXF_VERSION: ${{ matrix.NXF_VER }}
           # Skip sentieon tests - no ARM containers available
           SKIP_SENTIEON: true
-          # Skip parabricks tests - requires NVIDIA GPU
-          SKIP_PARABRICKS: true
+          # Skip GPU tests - requires NVIDIA GPU
+          SKIP_GPU: true
         with:
           profile: test,${{ matrix.profile }},${{ matrix.archProfile }}
           shard: ${{ matrix.shard }}

.github/workflows/nf-test.yml

@@ -45,8 +45,8 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
           # Skip sentieon tests on fork PRs where secrets are not available
           SKIP_SENTIEON: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name != 'nf-core/rnaseq' }}
-          # Skip parabricks/GPU tests on CPU runners
-          SKIP_PARABRICKS: "true"
+          # Skip GPU tests on CPU runners
+          SKIP_GPU: "true"
         with:
           max_shards: 20
 
@@ -100,8 +100,8 @@ jobs:
           NXF_VERSION: ${{ matrix.NXF_VER }}
           # Skip sentieon tests on fork PRs where secrets are not available
           SKIP_SENTIEON: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name != 'nf-core/rnaseq' }}
-          # Skip parabricks/GPU tests on CPU runners
-          SKIP_PARABRICKS: "true"
+          # Skip GPU tests on CPU runners
+          SKIP_GPU: "true"
         with:
           profile: test,${{ matrix.profile }}
           shard: ${{ matrix.shard }}

.nf-core.yml

@@ -27,4 +27,4 @@ template:
   name: rnaseq
   org: nf-core
   outdir: .
-  version: 3.24.0
+  version: 3.25.0

CHANGELOG.md

@@ -3,6 +3,44 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.25.0](https://github.com/nf-core/rnaseq/releases/tag/3.25.0)] - 2026-04-24
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Friederike Hanssen](https://github.com/FriederikeHanssen)
+- [James A. Fellows Yates](https://github.com/jfy133)
+- [Justin Payeur](https://github.com/Odulhin)
+- [Matthias Hörtenhuber](https://github.com/mashehu)
+- [Maxime U Garcia](https://github.com/maxulysse)
+- [Muhammad Imran](https://github.com/drimran87)
+- [Phil Ewels](https://github.com/ewels)
+- Weisheng Wu
+- [@wzheng0520](https://github.com/wzheng0520)
+
+### Enhancements and fixes
+
+- [PR #1755](https://github.com/nf-core/rnaseq/pull/1755) - Restructure `--stringtie_ignore_gtf` into a three-stage assemble → merge → quantify workflow via the nf-core `bam_stringtie_merge` subworkflow, publishing `stringtie_merge.gtf` and per-sample `<sample>.denovo.transcripts.gtf`
+- [PR #1781](https://github.com/nf-core/rnaseq/pull/1781) - Bump version to 3.25.0dev after release 3.24.0; fix SortMeRNA `%rRNA` appearing only under "Read 2" in MultiQC General Stats by using log filename for sample names instead of parsing paired-end read paths from log content
+- [PR #1784](https://github.com/nf-core/rnaseq/pull/1784) - Replace local `gtf2bed` module with nf-core `ea-utils/gtf2bed` module
+- [PR #1786](https://github.com/nf-core/rnaseq/pull/1786) - Replace local `bam_post_alignment_qc` subworkflow and `multiqc_custom_biotype` module with nf-core `bam_qc_rnaseq` subworkflow and `custom/multiqccustombiotype` module; update `dupradar` to topic-based version reporting
+- [PR #1788](https://github.com/nf-core/rnaseq/pull/1788) - Centralize pipeline-specific module configs in `conf/modules/` following the nf-core/sarek pattern
+- [PR #1790](https://github.com/nf-core/rnaseq/pull/1790) - Add `--use_gpu_ribodetector` parameter for GPU-accelerated rRNA removal with ribodetector; update ribodetector module to dual-container approach (x86 only); generalize GPU CI skip from `SKIP_PARABRICKS` to `SKIP_GPU`
+- [PR #1792](https://github.com/nf-core/rnaseq/pull/1792) - Always emit a strand-agnostic `<sample>.bigWig`. **Breaking**: per-strand bigWigs are no longer emitted for unstranded libraries, where a `-strand +/-` split carries no biological meaning ([#1275](https://github.com/nf-core/rnaseq/issues/1275))
+- [PR #1793](https://github.com/nf-core/rnaseq/pull/1793) - Scope MultiQC's `table_sample_merge` config to samplesheet paired-end IDs so samples with `_1`/`_2` suffixes (e.g. `foo_1`, `foo_2`) are no longer collapsed into a single `foo` row in General Statistics; factor MultiQC wiring into a new local `MULTIQC_RNASEQ` subworkflow
+- [PR #1795](https://github.com/nf-core/rnaseq/pull/1795) - Bump `custom/multiqccustombiotype` to fail loudly when the featureCounts output exceeds `--max_biotypes` (default 100), catching misconfigured `--featurecounts_group_type` values that previously hung MultiQC ([#424](https://github.com/nf-core/rnaseq/issues/424))
+- [PR #1796](https://github.com/nf-core/rnaseq/pull/1796) - Clarify prokaryotic profile docs: transcripts are extracted from all transcript-like features (CDS, tRNA, rRNA, tmRNA, ncRNA, etc.), not only CDS; CDS is only required for featureCounts biotype QC
+- [PR #1799](https://github.com/nf-core/rnaseq/pull/1799) - Bump version to 3.25.0 ahead of release
+- [PR #1803](https://github.com/nf-core/rnaseq/pull/1803) - Fix per-sample MultiQC hanging under `--skip_quantification_merge` by building the MultiQC input as a per-sample bundle, so each sample's report fires as soon as its own contributors arrive ([#1797](https://github.com/nf-core/rnaseq/issues/1797))
+- [PR #1804](https://github.com/nf-core/rnaseq/pull/1804) - Skip StringTie by default in the `prokaryotic` profile, where reference-guided transcript assembly is not informative for bacterial/archaeal annotations
+- [PR #1805](https://github.com/nf-core/rnaseq/pull/1805) - Add a new MultiQC "Strandedness checks" section whose table rows reflect which strandedness analyses actually ran for each sample; narrow the prokaryotic RSeQC skip to prokaryote-unsafe modules only
+- [PR #1806](https://github.com/nf-core/rnaseq/pull/1806) - Raise Bowtie2 default `-k` from 1 to 200 for `--aligner bowtie2_salmon` so Salmon's EM has enough multi-mapping evidence to quantify small transcriptomes correctly
+- [PR #1811](https://github.com/nf-core/rnaseq/pull/1811) - Update the default SortMeRNA rRNA database to `smr_v4.3_default_db` (SILVA 138) ([#1354](https://github.com/nf-core/rnaseq/issues/1354))
+- [PR #1812](https://github.com/nf-core/rnaseq/pull/1812) - Dedupe redundant pipeline-level nf-test cases (fold `min_mapped_reads` into `skip_qc`; prune duplicate pseudo-alignment cases) without losing coverage
+- [PR #1814](https://github.com/nf-core/rnaseq/pull/1814) - Sync nf-core components to the latest versions, migrate the remaining local `deseq2_qc` module to topic-based version reporting, and retire `ch_versions` plumbing now that all modules emit versions via topic
+- [PR #1815](https://github.com/nf-core/rnaseq/pull/1815) - Gate the nf-test `cleanup` directive on `$CI` so pipeline-test work directories are retained on local reruns and only pruned in CI ([#1813](https://github.com/nf-core/rnaseq/issues/1813))
+
 ## [[3.24.0](https://github.com/nf-core/rnaseq/releases/tag/3.24.0)] - 2026-04-09
 
 ### Credits

conf/arm.config

@@ -80,11 +80,11 @@ process {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e6db95013607b07689e38ee37a654d029236de77fdfde97fe1866f45d01e064/data' : 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' }
     }
 
-    withName: 'GTF2BED' {
+    withName: 'EAUTILS_GTF2BED' {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/89/896a3e55b2f664def0f8707420e1f53b4c447adb99fd6a1432a155c3403b9199/data' : 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' }
     }
 
-    withName: 'GTF_FILTER' {
+    withName: 'CUSTOM_GTFFILTER' {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' }
     }
 
@@ -120,8 +120,8 @@ process {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data' : 'community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8' }
     }
 
-    withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f0/f012a4fe624e7965c4c52fe1eb1b591a3d97cee5c16c5c0d654aa86ee1c0c801/data' : 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' }
+    withName: 'CUSTOM_MULTIQCCUSTOMBIOTYPE' {
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6e/6ed198a9c02e596e57c50cb2e497b279212c5b4e073fe9d0f7488a2877b019b8/data' : 'community.wave.seqera.io/library/python:3.12.12--bc40a6a9f24c35fa' }
     }
 
     withName: 'PICARD_MARKDUPLICATES' {
@@ -244,6 +244,10 @@ process {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9ebc6b1a27262420a5739330d369086b0d8c941a43b81d3fd0f741045bb3d46f/data' : 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' }
     }
 
+    withName: 'STRINGTIE_MERGE' {
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ff/ff41905fd891a7cdb392b85c230b417e8d4f43773ae13162c6fc6c3fca34b453/data' : 'community.wave.seqera.io/library/stringtie:2.2.1--104528d50906189c' }
+    }
+
     withName: 'SUBREAD_FEATURECOUNTS' {
         container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/2a/2a81571bc8c4ac812adb76c51045a245041d7cc8923a2d7cc34a866588fead0c/data' : 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' }
     }

subworkflows/local/align_bowtie2/nextflow.config → conf/modules/align_bowtie2.config

@@ -7,11 +7,22 @@ process {
         ext.args = {
             def args = [
                 '--very-sensitive',
-                '--no-discordant'
+                '--no-discordant',
+                '-k 200'
             ]
 
+            // Merge extras so user values override defaults (e.g. `-k N`).
+            // Must run before RG args since `--rg` repeats and would collapse.
             if (params.extra_bowtie2_align_args) {
-                args += [params.extra_bowtie2_align_args]
+                def baseMap = args.join(' ').split(/\s(?=-)/).collectEntries { String token ->
+                    def parts = token.trim().split(/\s+/, 2)
+                    [(parts[0]): parts.size() > 1 ? parts[1] : '']
+                }
+                def extraMap = params.extra_bowtie2_align_args.split(/\s(?=-)/).collectEntries { String token ->
+                    def parts = token.trim().split(/\s+/, 2)
+                    [(parts[0]): parts.size() > 1 ? parts[1] : '']
+                }
+                args = (baseMap + extraMap).collect { k, v -> v ? "${k} ${v}" : k }
             }
 
             // Read group tags - assembled once from samplesheet meta and pipeline params