Merge branch 'dev' into tx2gene-deterministic-resume

Author: pinin4fjords

.github/workflows/nf-test-gpu.yml

@@ -58,7 +58,7 @@ jobs:
 
   nf-test-gpu:
     needs: [get-shards]
-    runs-on: "runs-on=${{ github.run_id }}/family=g5.2xlarge/image=ubuntu24-gpu-x64"
+    runs-on: "runs-on=${{ github.run_id }}/family=g5.2xlarge+g6.2xlarge/image=ubuntu24-gpu-x64"
     name: "GPU Test | ${{ matrix.profile }} | ${{ matrix.shard }} | ${{ matrix.NXF_VER }} | ${{ matrix.filters }}"
     env:
       NXF_VER: ${{ matrix.NXF_VER }}

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1869](https://github.com/nf-core/rnaseq/pull/1869) - Add pipeline validation error when `--use_rustqc` and `--skip_markduplicates` are set together, since RustQC requires duplicate-marked BAM files ([#1865](https://github.com/nf-core/rnaseq/issues/1865))
 - [PR #1875](https://github.com/nf-core/rnaseq/pull/1875) - Select the tx2gene sample deterministically in `quant_tximport_summarizedexperiment` so the `CUSTOM_TX2GENE` cache survives `-resume` (nf-core/modules#12166)
 - [PR #1883](https://github.com/nf-core/rnaseq/pull/1883) - Update the `tximeta/tximport` module ([nf-core/modules#12362](https://github.com/nf-core/modules/pull/12362)): add a `jq` build dependency and set `LC_COLLATE=C` for reproducible gene-level output ordering
+- [PR #1884](https://github.com/nf-core/rnaseq/pull/1884) - Update `trimgalore` module to 2.3.0
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 

conf/arm.config

@@ -273,7 +273,7 @@ process {
     }
 
     withName: 'TRIMGALORE' {
-        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/e2/e23b3b324ac8b49a691ba4e74359846850ea082630e13b8ef0bc0392665efc33/data' : 'community.wave.seqera.io/library/trim-galore:2.1.0--7df2aae1e1928c85' }
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/06/0603053a9577911611d7b23a623f29959586c33792e6484d396e26cf09552fd9/data' : 'community.wave.seqera.io/library/trim-galore:2.3.0--41c957a42f06d443' }
     }
 
     withName: 'TXIMETA_TXIMPORT' {

modules.json

@@ -349,7 +349,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "0991b1032cccfcd9245ef59c6e56d6092ac0b3e7",
+                        "git_sha": "2a30bfb6a1b4667692d734e33e000a3bd1d74a0d",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
                     },
                     "tximeta/tximport": {

modules/nf-core/trimgalore/environment.yml

@@ -34,7 +34,7 @@
                     "samtools": "1.23.1"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "UNTAR_KRAKEN_DB": {
                     "untar": 1.34
@@ -139,7 +139,7 @@
                     "samtools": "1.23.1"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "UNTAR_HISAT2_INDEX": {
                     "untar": 1.34
@@ -236,7 +236,7 @@
                     "samtools": "1.23.1"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "UNTAR_KRAKEN_DB": {
                     "untar": 1.34
@@ -425,7 +425,7 @@
                     "subread": "2.0.6"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "TXIMETA_TXIMPORT": {
                     "bioconductor-tximeta": "1.20.1"
@@ -1814,7 +1814,7 @@
                     "subread": "2.0.6"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "TXIMETA_TXIMPORT": {
                     "bioconductor-tximeta": "1.20.1"
@@ -3107,7 +3107,7 @@
                     "samtools": "1.23.1"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "UNTAR_KRAKEN_DB": {
                     "untar": 1.34

modules/nf-core/trimgalore/main.nf

@@ -39,7 +39,7 @@
                     "star": "2.7.11b"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "UNTAR_SALMON_INDEX": {
                     "untar": 1.34
@@ -238,7 +238,7 @@
                     "subread": "2.0.6"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "TXIMETA_TXIMPORT": {
                     "bioconductor-tximeta": "1.20.1"

modules/nf-core/trimgalore/tests/main.nf.test.snap

@@ -36,7 +36,7 @@
                     "star": "2.7.11b"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "UNTAR_SALMON_INDEX": {
                     "untar": 1.34
@@ -162,7 +162,7 @@
                     "star": "2.7.11b"
                 },
                 "TRIMGALORE": {
-                    "trimgalore": "2.1.0"
+                    "trimgalore": "2.3.0"
                 },
                 "TXIMETA_TXIMPORT": {
                     "bioconductor-tximeta": "1.20.1"