diff --git a/CHANGELOG.md b/CHANGELOG.md
index d5c45983f..e683a96e3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ Special thanks to the following for their contributions to the release:
 
 - [PR #1608](https://github.com/nf-core/rnaseq/pull/1608) - Bump version after release 3.21.0
 - [PR #1617](https://github.com/nf-core/rnaseq/pull/1617) - Update bbmap/bbsplit module
+- [PR #1622](https://github.com/nf-core/rnaseq/pull/1622) - Update tximeta/tximport module to fix sample name mangling
 
 ## [[3.21.0](https://github.com/nf-core/rnaseq/releases/tag/3.21.0)] - 2025-09-18
 
diff --git a/modules.json b/modules.json
index 674b309c8..d5698b61c 100644
--- a/modules.json
+++ b/modules.json
@@ -269,7 +269,7 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "1f008221e451e7a4738226c49e69aaa2eb731369",
+                        "git_sha": "d205ebc03abc530a984d844ab57373f566967ac8",
                         "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 d4c6a5492..b8ab9bca8 100644
--- a/modules/nf-core/tximeta/tximport/meta.yml
+++ b/modules/nf-core/tximeta/tximport/meta.yml
@@ -25,9 +25,7 @@ input:
         description: |
           Groovy Map containing information related to the experiment as a whole
           e.g. `[ id:'SRP123456' ]`
-    - '"quants/*"':
-        type: directory
-        description: Directory containing quantification files
+    - quants/*: {}
   - - meta2:
         type: map
         description: |
@@ -37,12 +35,15 @@ input:
         type: file
         description: A transcript to gene mapping table such as those generated by custom/tx2gene
         pattern: "*.{csv,tsv}"
-  - - quant_type:
-        type: string
-        description: Quantification type, 'kallisto' or 'salmon'
+        ontologies:
+          - edam: http://edamontology.org/format_3752 # CSV
+          - edam: http://edamontology.org/format_3475 # TSV
+  - quant_type:
+      type: string
+      description: Quantification type, 'kallisto' or 'salmon'
 output:
-  - tpm_gene:
-      - meta:
+  tpm_gene:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -53,8 +54,10 @@ output:
             Abundance (TPM) values derived from tximport output after
             summarizeToGene(), without a 'countsFromAbundance' specification
           pattern: "*gene_tpm.tsv"
-  - counts_gene:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  counts_gene:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -65,8 +68,10 @@ output:
             Count values derived from tximport output after
             summarizeToGene(), without a 'countsFromAbundance' specification
           pattern: "*gene_counts.tsv"
-  - counts_gene_length_scaled:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  counts_gene_length_scaled:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -77,8 +82,10 @@ output:
             Count values derived from tximport output after summarizeToGene(), with
             a 'countsFromAbundance' specification of 'lengthScaledTPM'
           pattern: "*gene_counts_length_scaled.tsv"
-  - counts_gene_scaled:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  counts_gene_scaled:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -89,8 +96,10 @@ output:
             Count values derived from tximport output after summarizeToGene(), with
             a 'countsFromAbundance' specification of 'scaledTPM'
           pattern: "*gene_counts_scaled.tsv"
-  - lengths_gene:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  lengths_gene:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -101,8 +110,10 @@ output:
             Length values derived from tximport output after summarizeToGene(),
             without a 'countsFromAbundance' specification
           pattern: "*gene_lengths.tsv"
-  - tpm_transcript:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  tpm_transcript:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -113,8 +124,10 @@ output:
             Abundance (TPM) values derived from tximport output without
             summarizeToGene(), without a 'countsFromAbundance' specification
           pattern: "*transcript_tpm.tsv"
-  - counts_transcript:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  counts_transcript:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -125,8 +138,10 @@ output:
             Count values derived from tximport output without
             summarizeToGene(), without a 'countsFromAbundance' specification
           pattern: "*transcript_counts.tsv"
-  - lengths_transcript:
-      - meta:
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  lengths_transcript:
+    - - meta:
           type: map
           description: |
             Groovy Map containing information related to the experiment as a whole
@@ -137,11 +152,15 @@ output:
             Length values derived from tximport output without summarizeToGene(),
             without a 'countsFromAbundance' specification
           pattern: "*gene_lengths.tsv"
-  - versions:
-      - versions.yml:
-          type: file
-          description: File containing software versions
-          pattern: "versions.yml"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@pinin4fjords"
 maintainers:
diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r
index 5986c05d9..883935129 100755
--- a/modules/nf-core/tximeta/tximport/templates/tximport.r
+++ b/modules/nf-core/tximeta/tximport/templates/tximport.r
@@ -73,10 +73,10 @@ read_transcript_info <- function(tinfo_path){
     }
 
     transcript_info <- read.csv(tinfo_path, sep="\t", header = TRUE,
-                                col.names = c("tx", "gene_id", "gene_name"))
+                                col.names = c("tx", "gene_id", "gene_name"), 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))
+    transcript_info <- rbind(transcript_info, data.frame(tx=extra, gene_id=extra, gene_name=extra, check.names = FALSE))
     transcript_info <- transcript_info[match(rownames(txi[[1]]), transcript_info[["tx"]]), ]
     rownames(transcript_info) <- transcript_info[["tx"]]
 
@@ -131,7 +131,7 @@ txi <- tximport(fns, type = '$quant_type', txOut = TRUE, dropInfReps = dropInfRe
 transcript_info <- read_transcript_info('$tx2gene')
 
 # Make coldata just to appease the summarizedexperiment
-coldata <- data.frame(files = fns, names = names)
+coldata <- data.frame(files = fns, names = names, check.names = FALSE)
 rownames(coldata) <- coldata[["names"]]
 
 # Create initial SummarizedExperiment object