Merge pull request #1885 from pinin4fjords/fix/collect-ordering-determinism

Bump quant_tximport_summarizedexperiment and quantify_rsem for deterministic collect() ordering

Author: pinin4fjords

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 #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
+- [PR #1885](https://github.com/nf-core/rnaseq/pull/1885) - Bump `quant_tximport_summarizedexperiment` and `quantify_rsem` ([nf-core/modules#12377](https://github.com/nf-core/modules/pull/12377)): sort the collected per-sample inputs to `TXIMETA_TXIMPORT` and `CUSTOM_RSEMMERGECOUNTS` by staged file name, keeping their cache keys stable across `-resume` instead of following non-deterministic task-completion order ([#1879](https://github.com/nf-core/rnaseq/issues/1879))
 
 ## [[3.26.0](https://github.com/nf-core/rnaseq/releases/tag/3.26.0)] - 2026-05-07
 

modules.json

@@ -483,7 +483,7 @@
                     },
                     "quant_tximport_summarizedexperiment": {
                         "branch": "master",
-                        "git_sha": "77df703775155f3f0f8922f9354501e0289348c2",
+                        "git_sha": "fbf6cd41f577f23d33a2d8354f6d8b4feafdffe0",
                         "installed_by": ["quantify_pseudo_alignment", "quantify_rsem"]
                     },
                     "quantify_pseudo_alignment": {
@@ -493,7 +493,7 @@
                     },
                     "quantify_rsem": {
                         "branch": "master",
-                        "git_sha": "77378d340769713877b6a7f72fb7b66f89e65a4c",
+                        "git_sha": "fbf6cd41f577f23d33a2d8354f6d8b4feafdffe0",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {