Merge pull request #1560 from nf-core/add_trimgalore_stats_fix

General modules update, include updating subworkflows for stats fixes

Author: pinin4fjords

CHANGELOG.md

@@ -7,6 +7,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Credits
 
+Special thanks to the following for their contributions to the release:
+
+- [Alena Nikolaeva](https://github.com/AlenaNik)
+- [Anabella Trigila](https://github.com/atrigila)
+- [Angel Pizarro](https://github.com/delagoya)
+- [Ben Sherman](https://github.com/bentsherman)
+- [Dave Carlson](https://github.com/davidecarlson)
+- [Gabriel Lichtenstein](https://github.com/glichtenstein)
+- [Lorenzo Fontana](https://github.com/fntlnz)
+- [Matthias Hörtenhuber](https://github.com/mashehu)
+- [Milos Micik](https://github.com/milos7250)
+- [Maxime Garcia](https://github.com/maxulysse)
+
 ### Enhancements & fixes
 
 - [PR #1480](https://github.com/nf-core/rnaseq/pull/1480) - Bump version after release 3.18.0
@@ -23,6 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #1553](https://github.com/nf-core/rnaseq/pull/1553) - Make jobs automatically resubmit for exit code 175
 - [PR #1556](https://github.com/nf-core/rnaseq/pull/1556) - Update index docs to remove references to 'indexing only mode'
 - [PR #1558](https://github.com/nf-core/rnaseq/pull/1558) - Remove patches and bump modules for ARM compat
+- [PR #1560](https://github.com/nf-core/rnaseq/pull/1560) - General modules update, include updating subworkflows for stats fixes
 
 # 3.18.0 - 2024-12-19
 

modules.json

@@ -36,7 +36,8 @@ process STAR_ALIGN_IGENOMES {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads1 = [], reads2 = []
+    def reads1 = []
+    def reads2 = []
     meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
     def ignore_gtf      = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
     def seq_platform    = seq_platform ? "'PL:$seq_platform'" : ""