Merge branch 'dev' into interface_to_kmer

Author: pinin4fjords

CHANGELOG.md

@@ -7,11 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Credits
 
-### Enhancements & fixes
+Special thanks to the following for their contributions to the release:
 
-- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling.
-- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
-- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)
+- [Matthias Zepper](https://github.com/MatthiasZepper)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Phil Ewels](https://github.com/ewels)
+- [Vlad Savelyev](https://github.com/vladsavelyev)
 
 ### Parameters
 
@@ -23,9 +27,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 > **NB:** Parameter has been **added** if just the new parameter information is present.
 > **NB:** Parameter has been **removed** if new parameter information isn't present.
 
-### Software dependencies
+### Enhancements & fixes
 
-### Modules / Subworkflows
+- [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling
+- [PR #1141](https://github.com/nf-core/rnaseq/pull/1141) - Important! Template update for nf-core/tools v2.11
+- [PR #1149](https://github.com/nf-core/rnaseq/pull/1149) - Fix and patch version commands for Fastp, FastQC and UMI-tools modules ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
+- [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners
 
 ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
 

modules.json

@@ -28,12 +28,14 @@
                     "fastp": {
                         "branch": "master",
                         "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"],
+                        "patch": "modules/nf-core/fastp/fastp.diff"
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
-                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
+                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"],
+                        "patch": "modules/nf-core/fastqc/fastqc.diff"
                     },
                     "fq/subsample": {
                         "branch": "master",
@@ -222,12 +224,14 @@
                     "umitools/dedup": {
                         "branch": "master",
                         "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
-                        "installed_by": ["bam_dedup_stats_samtools_umitools"]
+                        "installed_by": ["bam_dedup_stats_samtools_umitools"],
+                        "patch": "modules/nf-core/umitools/dedup/umitools-dedup.diff"
                     },
                     "umitools/extract": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"],
+                        "patch": "modules/nf-core/umitools/extract/umitools-extract.diff"
                     },
                     "untar": {
                         "branch": "master",