diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0e589231..5c0e40916 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r
index d55180400..003b6852c 100755
--- a/bin/deseq2_qc.r
+++ b/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)))
diff --git a/modules.json b/modules.json
index dd4cb5309..4589b12db 100644
--- a/modules.json
+++ b/modules.json
@@ -269,7 +269,7 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "d205ebc03abc530a984d844ab57373f566967ac8",
+                        "git_sha": "9ef7553c32b02bc33ecb962b5f07a8cb16b2117c",
                         "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "ucsc/bedclip": {
diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml
index b8ab9bca8..16519f17d 100644
--- a/modules/nf-core/tximeta/tximport/meta.yml
+++ b/modules/nf-core/tximeta/tximport/meta.yml
@@ -25,7 +25,11 @@ input:
         description: |
           Groovy Map containing information related to the experiment as a whole
           e.g. `[ id:'SRP123456' ]`
-    - quants/*: {}
+    - "quants/*":
+        type: file
+        description: |
+          Quantification files
+
   - - meta2:
         type: map
         description: |
@@ -40,7 +44,7 @@ input:
           - edam: http://edamontology.org/format_3475 # TSV
   - quant_type:
       type: string
-      description: Quantification type, 'kallisto' or 'salmon'
+      description: Quantification type, `kallisto` or `salmon`
 output:
   tpm_gene:
     - - meta:
diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r
index 883935129..0ff05ef04 100755
--- a/modules/nf-core/tximeta/tximport/templates/tximport.r
+++ b/modules/nf-core/tximeta/tximport/templates/tximport.r
@@ -14,6 +14,23 @@ library(tximport)
 ################################################
 ################################################
 
+#' Parse out options from a string without recourse to optparse
+#'
+#' @param x Long-form argument list like --opt1 val1 --opt2 val2
+#'
+#' @return named list of options and values similar to optparse
+
+parse_args <- function(x){
+    args_list <- unlist(strsplit(x, ' ?--')[[1]])[-1]
+    args_vals <- lapply(args_list, function(y) scan(text=y, what='character', quiet = TRUE))
+
+    # Ensure the option vectors are length 2 (key/value) to catch empty ones
+    args_vals <- lapply(args_vals, function(z){ length(z) <- 2; z})
+
+    parsed_args <- structure(lapply(args_vals, function(y) y[2]), names = lapply(args_vals, function(y) y[1]))
+    parsed_args[! is.na(parsed_args)]
+}
+
 #' Build a table from a SummarizedExperiment object
 #'
 #' This function takes a SummarizedExperiment object and a specific slot name to extract
@@ -53,27 +70,38 @@ write_se_table <- function(params, prefix) {
 #' Read Transcript Metadata from a Given Path
 #'
 #' This function reads transcript metadata from a specified file path. The file is expected to
-#' be a tab-separated values file without headers, containing transcript information. The function
-#' checks if the file is empty and stops execution with an error message if so. It reads the file
-#' into a data frame, expecting columns for transcript IDs, gene IDs, and gene names. Additional
+#' be a tab-separated values file with a header, containing transcript information. Columns are
+#' selected by name using the tx_col, gene_id_col, and gene_name_col parameters. The function
+#' checks if the file is empty and stops execution with an error message if so. Additional
 #' processing is done to ensure compatibility with a predefined data structure (e.g., `txi[[1]]`),
 #' including adding missing entries and reordering based on the transcript IDs found in `txi[[1]]`.
 #'
 #' @param tinfo_path The file path to the transcript information file.
+#' @param tx_col Column name for transcript IDs.
+#' @param gene_id_col Column name for gene IDs.
+#' @param gene_name_col Column name for gene names.
 #'
 #' @return A list containing three elements:
 #' - `transcript`: A data frame with transcript IDs, gene IDs, and gene names, indexed by transcript IDs.
 #' - `gene`: A data frame with unique gene IDs and gene names.
 #' - `tx2gene`: A data frame mapping transcript IDs to gene IDs.
 
-read_transcript_info <- function(tinfo_path){
+read_transcript_info <- function(tinfo_path, tx_col, gene_id_col, gene_name_col){
     info <- file.info(tinfo_path)
     if (info\$size == 0) {
         stop("tx2gene file is empty")
     }
 
-    transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE,
-                                col.names = c("tx", "gene_id", "gene_name"), check.names = FALSE)
+    # Read file with actual header to handle variable column counts correctly
+    raw_info <- read.csv(tinfo_path, sep="\t", header = TRUE, check.names = FALSE)
+
+    # Select columns by name, falling back to position if name not found
+    transcript_info <- data.frame(
+        tx = raw_info[[if (tx_col %in% colnames(raw_info)) tx_col else 1]],
+        gene_id = raw_info[[if (gene_id_col %in% colnames(raw_info)) gene_id_col else 2]],
+        gene_name = raw_info[[if (gene_name_col %in% colnames(raw_info)) gene_name_col else 3]],
+        check.names = FALSE
+    )
 
     extra <- setdiff(rownames(txi[[1]]), as.character(transcript_info[["tx"]]))
     transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra, check.names = FALSE))
@@ -117,6 +145,21 @@ create_summarized_experiment <- function(counts, abundance, length, col_data, ro
 ################################################
 ################################################
 
+# Set defaults and classes
+opt <- list(
+    tx_col = "transcript_id",
+    gene_id_col = "gene_id",
+    gene_name_col = "gene_name"
+)
+
+# Apply parameter overrides from ext.args
+args_opt <- parse_args('$task.ext.args')
+for (ao in names(args_opt)) {
+    if (ao %in% names(opt)) {
+        opt[[ao]] <- args_opt[[ao]]
+    }
+}
+
 # Define pattern for file names based on quantification type
 pattern <- ifelse('$quant_type' == "kallisto", "abundance.tsv", "quant.sf")
 fns <- list.files('quants', pattern = pattern, recursive = T, full.names = T)
@@ -128,7 +171,7 @@ dropInfReps <- '$quant_type' == "kallisto"
 txi <- tximport(fns, type = '$quant_type', txOut = TRUE, dropInfReps = dropInfReps)
 
 # Read transcript and sample data
-transcript_info <- read_transcript_info('$tx2gene')
+transcript_info <- read_transcript_info('$tx2gene', opt\$tx_col, opt\$gene_id_col, opt\$gene_name_col)
 
 # Make coldata just to appease the summarizedexperiment
 coldata <- data.frame(files = fns, names = names, check.names = FALSE)
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test b/modules/nf-core/tximeta/tximport/tests/main.nf.test
index 9bdb7fd46..5e3b50b26 100644
--- a/modules/nf-core/tximeta/tximport/tests/main.nf.test
+++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test
@@ -4,6 +4,12 @@ nextflow_process {
     script "../main.nf"
     process "TXIMETA_TXIMPORT"
 
+    tag "modules"
+    tag "modules_nfcore"
+    tag "custom/tx2gene"
+    tag "tximeta"
+    tag "tximeta/tximport"
+    tag "untar"
 
     test("saccharomyces_cerevisiae - kallisto - gtf") {
 
@@ -65,9 +71,7 @@ nextflow_process {
         }
     }
 
-    test("saccharomyces_cerevisiae - kallisto - gtf - stub") {
-
-        options "-stub"
+    test("saccharomyces_cerevisiae - kallisto - gtf - extra_attributes") {
 
         setup {
             run("UNTAR") {
@@ -92,12 +96,44 @@ nextflow_process {
                     input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
                     input[2] = 'kallisto'
                     input[3] = 'gene_id'
-                    input[4] = 'gene_name'
+                    input[4] = 'gene_name,gene_biotype'
                     """
                 }
             }
         }
 
+        when {
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = 'kallisto'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.counts_gene,
+                    process.out.counts_gene_length_scaled,
+                    process.out.counts_gene_scaled,
+                    process.out.counts_transcript,
+                    process.out.lengths_gene,
+                    process.out.lengths_transcript,
+                    process.out.tpm_gene,
+                    process.out.tpm_transcript,
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
+
+    test("saccharomyces_cerevisiae - kallisto - gtf - stub") {
+
+        options "-stub"
+
         when {
             process {
                 """
@@ -228,4 +264,66 @@ nextflow_process {
             )
         }
     }
+
+    test("saccharomyces_cerevisiae - kallisto - gtf - custom_column_names") {
+
+        config "./nextflow.config"
+
+        setup {
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/kallisto_results.tar.gz', checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+            run("CUSTOM_TX2GENE") {
+                script "../../../custom/tx2gene/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of([
+                        [ id:'test'], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/eukaryotes/saccharomyces_cerevisiae/genome_gfp.gtf', checkIfExists: true)
+                    ])
+                    input[1] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                    input[2] = 'kallisto'
+                    input[3] = 'gene_id'
+                    input[4] = 'gene_name,gene_biotype'
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                // Uses ext.args = '--gene_name_col gene_biotype' from nextflow.config
+                input[0] = UNTAR.out.untar.map { meta, dir -> [ meta, dir.listFiles().collect() ] }
+                input[1] = CUSTOM_TX2GENE.out.tx2gene
+                input[2] = 'kallisto'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.counts_gene,
+                    process.out.counts_gene_length_scaled,
+                    process.out.counts_gene_scaled,
+                    process.out.counts_transcript,
+                    process.out.lengths_gene,
+                    process.out.lengths_transcript,
+                    process.out.tpm_gene,
+                    process.out.tpm_transcript,
+                    process.out.versions).match()
+                }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
index 71ce1293e..cff6b0023 100644
--- a/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
+++ b/modules/nf-core/tximeta/tximport/tests/main.nf.test.snap
@@ -5,7 +5,7 @@
                 "0": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -13,7 +13,7 @@
                 "1": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -21,7 +21,7 @@
                 "2": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -29,7 +29,7 @@
                 "3": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -37,7 +37,7 @@
                 "4": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -45,7 +45,7 @@
                 "5": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -53,7 +53,7 @@
                 "6": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -61,7 +61,7 @@
                 "7": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -72,7 +72,7 @@
                 "counts_gene": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -80,7 +80,7 @@
                 "counts_gene_length_scaled": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -88,7 +88,7 @@
                 "counts_gene_scaled": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -96,7 +96,7 @@
                 "counts_transcript": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -104,7 +104,7 @@
                 "lengths_gene": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -112,7 +112,7 @@
                 "lengths_transcript": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -120,7 +120,7 @@
                 "tpm_gene": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -128,7 +128,7 @@
                 "tpm_transcript": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -140,9 +140,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-12-17T19:24:48.684346976"
+        "timestamp": "2025-12-09T09:26:21.185522"
     },
     "saccharomyces_cerevisiae - salmon - gtf": {
         "content": [
@@ -216,85 +216,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-12-17T19:24:59.699008761"
-    },
-    "saccharomyces_cerevisiae - kallisto - gtf": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gene_counts.tsv:md5,e89c28692ea214396b2d4cb702a804c3"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gene_counts_length_scaled.tsv:md5,4944841ac711124d29673b6b6ed16ef3"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gene_counts_scaled.tsv:md5,39d14e361434978b3cadae901a26a028"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.transcript_counts.tsv:md5,42e0106e75fa97c1c684c6d9060f1724"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gene_lengths.tsv:md5,db6becdf807fd164a9c63dd1dd916d9c"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.transcript_lengths.tsv:md5,f974b52840431a5dae57bcb615badbf1"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.gene_tpm.tsv:md5,85d108269769ae0d841247b9b9ed922d"
-                ]
-            ],
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.transcript_tpm.tsv:md5,65862ed9d4a05abfab952e680dc0e49d"
-                ]
-            ],
-            [
-                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
-        },
-        "timestamp": "2024-12-17T19:24:36.406126268"
+        "timestamp": "2025-12-09T09:27:19.912432"
     },
     "saccharomyces_cerevisiae - salmon - gtf - stub": {
         "content": [
@@ -302,7 +226,7 @@
                 "0": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -310,7 +234,7 @@
                 "1": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -318,7 +242,7 @@
                 "2": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -326,7 +250,7 @@
                 "3": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -334,7 +258,7 @@
                 "4": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -342,7 +266,7 @@
                 "5": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -350,7 +274,7 @@
                 "6": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -358,7 +282,7 @@
                 "7": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -369,7 +293,7 @@
                 "counts_gene": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -377,7 +301,7 @@
                 "counts_gene_length_scaled": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_length_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -385,7 +309,7 @@
                 "counts_gene_scaled": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_counts_scaled.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -393,7 +317,7 @@
                 "counts_transcript": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -401,7 +325,7 @@
                 "lengths_gene": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -409,7 +333,7 @@
                 "lengths_transcript": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_lengths.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -417,7 +341,7 @@
                 "tpm_gene": [
                     [
                         [
-
+                            
                         ],
                         "[].gene_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -425,7 +349,7 @@
                 "tpm_transcript": [
                     [
                         [
-
+                            
                         ],
                         "[].transcript_tpm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -437,8 +361,236 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-09T09:28:42.817097"
+    },
+    "saccharomyces_cerevisiae - kallisto - gtf - custom_column_names": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,acb4437b0298590f1b9a32a090433ede"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,e17a3ab77900d63af813d05e9edf48cb"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,09d7d12038b6616fa72a1d671ec9cf22"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,42e0106e75fa97c1c684c6d9060f1724"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,e326b39633bfc0ab61e112627d5362a9"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,f974b52840431a5dae57bcb615badbf1"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,ef2da5c832e4d126bca09464cab756b6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,65862ed9d4a05abfab952e680dc0e49d"
+                ]
+            ],
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-09T09:29:35.461954"
+    },
+    "saccharomyces_cerevisiae - kallisto - gtf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,e89c28692ea214396b2d4cb702a804c3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,4944841ac711124d29673b6b6ed16ef3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,39d14e361434978b3cadae901a26a028"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,42e0106e75fa97c1c684c6d9060f1724"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,db6becdf807fd164a9c63dd1dd916d9c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,f974b52840431a5dae57bcb615badbf1"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,85d108269769ae0d841247b9b9ed922d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,65862ed9d4a05abfab952e680dc0e49d"
+                ]
+            ],
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-12-09T09:23:53.102679"
+    },
+    "saccharomyces_cerevisiae - kallisto - gtf - extra_attributes": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts.tsv:md5,e89c28692ea214396b2d4cb702a804c3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_length_scaled.tsv:md5,4944841ac711124d29673b6b6ed16ef3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_counts_scaled.tsv:md5,39d14e361434978b3cadae901a26a028"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_counts.tsv:md5,42e0106e75fa97c1c684c6d9060f1724"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_lengths.tsv:md5,db6becdf807fd164a9c63dd1dd916d9c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_lengths.tsv:md5,f974b52840431a5dae57bcb615badbf1"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.gene_tpm.tsv:md5,85d108269769ae0d841247b9b9ed922d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.transcript_tpm.tsv:md5,65862ed9d4a05abfab952e680dc0e49d"
+                ]
+            ],
+            [
+                "versions.yml:md5,6ff317cceddc686f84d79cb976e1e28b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-12-17T19:25:16.373218283"
+        "timestamp": "2025-12-09T09:24:47.963548"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/tximeta/tximport/tests/nextflow.config b/modules/nf-core/tximeta/tximport/tests/nextflow.config
new file mode 100644
index 000000000..766d98ff9
--- /dev/null
+++ b/modules/nf-core/tximeta/tximport/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'TXIMETA_TXIMPORT' {
+        ext.args = '--gene_name_col gene_biotype'
+    }
+}
diff --git a/workflows/rnaseq/assets/multiqc/multiqc_config.yml b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
index bd24bc156..ee909f7d5 100644
--- a/workflows/rnaseq/assets/multiqc/multiqc_config.yml
+++ b/workflows/rnaseq/assets/multiqc/multiqc_config.yml
@@ -75,6 +75,7 @@ report_section_order:
     order: -1002
 
 export_plots: true
+export_plots_timeout: 60
 disable_version_detection: true
 sample_names_replace_exact: true