From 11f0c738d582870a18ba47c7cab3e5eaae140d5c Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 4 Sep 2024 11:09:15 +0100
Subject: [PATCH 1/2] Bump tximeta/tximport for gene table rownames fix

---
 modules.json                                          | 2 +-
 modules/nf-core/tximeta/tximport/templates/tximport.r | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules.json b/modules.json
index c5561e558..6e266bc86 100644
--- a/modules.json
+++ b/modules.json
@@ -237,7 +237,7 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "af778cca88b2a983152bdf2d80634e52dd1ef80f",
+                        "git_sha": "d612c281cf2fae62cdd79c70a22fc6349108570c",
                         "installed_by": ["modules", "quantify_pseudo_alignment"]
                     },
                     "ucsc/bedclip": {
diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r
index 510cfac59..e8235c8b0 100755
--- a/modules/nf-core/tximeta/tximport/templates/tximport.r
+++ b/modules/nf-core/tximeta/tximport/templates/tximport.r
@@ -153,7 +153,7 @@ if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info\$tx2gene))
     gi.s <- summarizeToGene(txi, tx2gene = tx2gene, countsFromAbundance = "scaledTPM")
 
     gene_info <- transcript_info\$gene[match(rownames(gi[[1]]), transcript_info\$gene[["gene_id"]]),]
-
+    rownames(gene_info) <- NULL
     col_data_frame <- DataFrame(coldata)
 
     # Create gene-level SummarizedExperiment objects

From 59988f8ba3a555303632c95a0e78192d2faa9e1a Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 4 Sep 2024 11:11:45 +0100
Subject: [PATCH 2/2] Update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23eb1fe16..2c3d147f3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -126,6 +126,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1367](https://github.com/nf-core/rnaseq/pull/1367) - Clarify design formula and blind dispersion estimation
 - [PR #1370](https://github.com/nf-core/rnaseq/pull/1370) - Bump versions for 3.15.0
 - [PR #1371](https://github.com/nf-core/rnaseq/pull/1371) - Apply Maxime's CHANGELOG edits
+- [PR #1372](https://github.com/nf-core/rnaseq/pull/1372) - Bump tximeta/tximport for gene table row names fix
 
 ### Parameters