Merge pull request #1662 from nf-core/dev

Dev -> master for nf-core/rnaseq 3.22.2

Author: pinin4fjords

.nf-core.yml

@@ -22,4 +22,4 @@ template:
   name: rnaseq
   org: nf-core
   outdir: .
-  version: 3.22.1
+  version: 3.22.2

CHANGELOG.md

@@ -3,6 +3,27 @@
 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).
 
+## [[3.22.2](https://github.com/nf-core/rnaseq/releases/tag/3.22.2)] - 2025-12-11
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [ahwanpandey](https://github.com/ahwanpandey)
+- [Graeme Grimes](https://github.com/ggrimes)
+- [Pontus Höjer](https://github.com/pontushojer)
+
+### Enhancements and fixes
+
+- [PR #1654](https://github.com/nf-core/rnaseq/pull/1654) - Fix tximport to handle tx2gene files with extra columns from `--gtf_extra_attributes`, and fix sample name mangling in DESeq2 QC
+- [PR #1655](https://github.com/nf-core/rnaseq/pull/1655) - Fix duplicate flagstat files in MultiQC report when mark duplicates is enabled ([#1653](https://github.com/nf-core/rnaseq/issues/1653))
+- [PR #1656](https://github.com/nf-core/rnaseq/pull/1656) - Bump version after release 3.22.1
+- [PR #1659](https://github.com/nf-core/rnaseq/pull/1659) - Fix MultiQC sample name collisions when multiple samples share the same FASTQ filename ([#1657](https://github.com/nf-core/rnaseq/issues/1657))
+- [PR #1658](https://github.com/nf-core/rnaseq/pull/1658) - Bump nf-core/multiqc module to 1.33
+- [PR #1660](https://github.com/nf-core/rnaseq/pull/1660) - Update MultiQC ARM container to 1.33
+- [PR #1648](https://github.com/nf-core/rnaseq/pull/1648) - Reduce duplicate coverage in pipeline tests by adding skip options
+- [PR #1661](https://github.com/nf-core/rnaseq/pull/1661) - Bump version to 3.22.2 ahead of release
+
 ## [[3.22.1](https://github.com/nf-core/rnaseq/releases/tag/3.22.1)] - 2025-12-04
 
 ### Credits

bin/deseq2_qc.r

@@ -55,7 +55,7 @@ if (is.null(opt$count_file)){
 ################################################
 ################################################
 
-count.table           <- read.delim(file=opt$count_file,header=TRUE, row.names=NULL)
+count.table           <- read.delim(file=opt$count_file,header=TRUE, row.names=NULL, check.names=FALSE)
 rownames(count.table) <- count.table[,opt$id_col]
 count.table           <- count.table[,opt$count_col:ncol(count.table),drop=FALSE]
 colnames(count.table) <- gsub(opt$sample_suffix,"",colnames(count.table))
@@ -76,7 +76,7 @@ samples.vec     <- colnames(count.table)
 name_components <- strsplit(samples.vec, "_")
 n_components    <- length(name_components[[1]])
 decompose       <- n_components!=1 && all(sapply(name_components, length)==n_components)
-coldata         <- data.frame(samples.vec, sample=samples.vec, row.names=1)
+coldata         <- data.frame(sample=samples.vec, row.names=samples.vec)
 if (decompose) {
     groupings        <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
     n_distinct       <- sapply(groupings, function(grp) length(unique(grp)))

conf/arm.config

@@ -109,7 +109,7 @@ process {
     }
 
     withName: 'MULTIQC' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c8a4a71510e6ef370a48bb155b32ad1cb00a053431986bae06f97361598c50b3/data' : 'community.wave.seqera.io/library/multiqc:1.31--e89b9d3faf1041af' }
+        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' {

modules.json

@@ -108,7 +108,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "e10b76ca0c66213581bec2833e30d31f239dec0b",
+                        "git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
                         "installed_by": ["modules"]
                     },
                     "picard/markduplicates": {
@@ -269,7 +269,7 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "d205ebc03abc530a984d844ab57373f566967ac8",
+                        "git_sha": "9ef7553c32b02bc33ecb962b5f07a8cb16b2117c",
                         "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "ucsc/bedclip": {