Merge remote-tracking branch 'origin/dev' into update-trimgalore

# Conflicts:
#	CHANGELOG.md

Author: pinin4fjords

CHANGELOG.md

@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1862](https://github.com/nf-core/rnaseq/pull/1862) - Correct the `docs/usage.md` note to state that `--extra_star_align_args` applies to `--aligner star_rsem`, since STAR runs as a standalone step and RSEM quantifies the resulting BAM ([#1857](https://github.com/nf-core/rnaseq/issues/1857))
 - [PR #1864](https://github.com/nf-core/rnaseq/pull/1864) - Bump nf-schema to 2.7.2, fixing boolean CLI parameter validation failures under Nextflow 26.x strict syntax ([#1860](https://github.com/nf-core/rnaseq/issues/1860))
 - [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 #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

modules.json

@@ -354,7 +354,7 @@
                     },
                     "tximeta/tximport": {
                         "branch": "master",
-                        "git_sha": "77df703775155f3f0f8922f9354501e0289348c2",
+                        "git_sha": "2e17764b67b7613c0a420c3f13d9360c3377bee8",
                         "installed_by": ["quant_tximport_summarizedexperiment", "quantify_pseudo_alignment"]
                     },
                     "ucsc/bedclip": {

modules/nf-core/tximeta/tximport/environment.yml

@@ -1829,11 +1829,11 @@
                 "WT_REP2.biotype_counts_mqc.tsv:md5,c04c2936bbfac3bff284f96b7233b158",
                 "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
                 "WT_REP2.featureCounts.tsv:md5,da2c6d621864e2f26958e2c299708c3e",
-                "rsem.merged.gene_counts.tsv:md5,060949cead024e393378bec58c82c976",
-                "rsem.merged.gene_counts_length_scaled.tsv:md5,8ceb1a2f0662630ad658d565db50c852",
-                "rsem.merged.gene_counts_scaled.tsv:md5,fdc2bb1618019953151b053107293543",
-                "rsem.merged.gene_lengths.tsv:md5,5b43d4327096c8714351fa3b147ace4b",
-                "rsem.merged.gene_tpm.tsv:md5,b4b1a0f093a5be3f43e2a5f583138709",
+                "rsem.merged.gene_counts.tsv:md5,43ac77bb055be372ee42deb5ec0199f6",
+                "rsem.merged.gene_counts_length_scaled.tsv:md5,58040cecbc89aee6e7b53761bfad19ef",
+                "rsem.merged.gene_counts_scaled.tsv:md5,7873cf3b356435d6175ff4821288be0d",
+                "rsem.merged.gene_lengths.tsv:md5,6455b4186bdf2e786017724bc00966d8",
+                "rsem.merged.gene_tpm.tsv:md5,72aa275645fde43a528e42b254285b32",
                 "rsem.merged.transcript_counts.tsv:md5,058a1780f4e0622c0cffb38ff7dcb66a",
                 "rsem.merged.transcript_lengths.tsv:md5,abcbf186029d6accc817a5b84a71e650",
                 "rsem.merged.transcript_tpm.tsv:md5,2368b7b8e5561ff2d5a0672bb2f0301b",
@@ -1872,7 +1872,7 @@
                 "i_data.ctab:md5,7e81ace0a68bfe42482420b7275de195"
             ]
         ],
-        "timestamp": "2026-05-01T16:23:34.874577699",
+        "timestamp": "2026-07-15T12:50:56.239252039",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"

modules/nf-core/tximeta/tximport/main.nf

@@ -1237,11 +1237,11 @@
                 "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1eb030549d877ab7fa51fe1d632ffe09",
                 "WT_REP1.SJ.out.tab:md5,5292020e46d35c14354f13696bbf0ab0",
                 "WT_REP2.SJ.out.tab:md5,3fab08b47b8b3cab91ae91dec8750152",
-                "rsem.merged.gene_counts.tsv:md5,91223fb1d835d6bc5140a5e095ad5b3e",
-                "rsem.merged.gene_counts_length_scaled.tsv:md5,ec0e98882128ff058169354fd1ccb240",
-                "rsem.merged.gene_counts_scaled.tsv:md5,59ec3256b6ecf3c58d9a86c6dfde51fd",
-                "rsem.merged.gene_lengths.tsv:md5,acdee55d5bd05d5cc83e4ca029b960b2",
-                "rsem.merged.gene_tpm.tsv:md5,8068aa3bb3369b818af7ece24977d8da",
+                "rsem.merged.gene_counts.tsv:md5,889e45a0d9cc2e069016305129a13f01",
+                "rsem.merged.gene_counts_length_scaled.tsv:md5,84a6fa0aad14b7bee4754af5e677d0b2",
+                "rsem.merged.gene_counts_scaled.tsv:md5,e86894ecc50dec68b979191898b7c9f6",
+                "rsem.merged.gene_lengths.tsv:md5,273ca6d2b937af63539c088fc4854a8c",
+                "rsem.merged.gene_tpm.tsv:md5,fecf349b2d3a267fd91c5cd45e4e8592",
                 "rsem.merged.transcript_counts.tsv:md5,535ab7cf11f6efde878283dc722dea0b",
                 "rsem.merged.transcript_lengths.tsv:md5,cb304a9c4932075da049cea5fe2a8165",
                 "rsem.merged.transcript_tpm.tsv:md5,8fe690a435900ef5a3c1cf639192ac5d",
@@ -1280,7 +1280,7 @@
                 "i_data.ctab:md5,7e81ace0a68bfe42482420b7275de195"
             ]
         ],
-        "timestamp": "2026-05-01T16:41:18.904088528",
+        "timestamp": "2026-07-15T12:54:17.149160947",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"