fix(tximport): handle tx2gene files with extra columns

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### 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 #1658](https://github.com/nf-core/rnaseq/pull/1658) - Bump nf-core/multiqc module to 1.33

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)))

modules.json

@@ -269,7 +269,7 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "d205ebc03abc530a984d844ab57373f566967ac8",
+                        "git_sha": "9ef7553c32b02bc33ecb962b5f07a8cb16b2117c",
                         "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "ucsc/bedclip": {