Merge pull request #1152 from drpatelh/fixes

Bump container versions for tools using Docker V1 manifest

CHANGELOG.md

@@ -26,6 +26,7 @@ Special thanks to the following for their contributions to the release:
 - [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 #1150](https://github.com/nf-core/rnaseq/pull/1150) - Be more flexible on attribute values in GTFs ([#1132](https://github.com/nf-core/rnaseq/issues/1132))
 - [PR #1151](https://github.com/nf-core/rnaseq/pull/1151) - fix to #1150: reinstate conditional
+- [PR #1152](https://github.com/nf-core/rnaseq/pull/1152) - Bump container versions for tools using Docker V1 manifest ([#1140](https://github.com/nf-core/rnaseq/issues/1140))
 
 ### Parameters
 
@@ -37,6 +38,19 @@ Special thanks to the following for their contributions to the release:
 > **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
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `qualimap` | 2.2.2d      | 2.3         |
+| `rseqc`    | 3.0.1       | 5.0.3       |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
 
 ### Credits

modules.json

@@ -90,7 +90,8 @@
                     "qualimap/rnaseq": {
                         "branch": "master",
                         "git_sha": "4657d98bc9f565e067c4d924126ce107056f5e2f",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff"
                     },
                     "rsem/calculateexpression": {
                         "branch": "master",
@@ -105,42 +106,50 @@
                     "rseqc/bamstat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff"
                     },
                     "rseqc/inferexperiment": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff"
                     },
                     "rseqc/innerdistance": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff"
                     },
                     "rseqc/junctionannotation": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff"
                     },
                     "rseqc/junctionsaturation": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff"
                     },
                     "rseqc/readdistribution": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff"
                     },
                     "rseqc/readduplication": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff"
                     },
                     "rseqc/tin": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_rseqc"]
+                        "installed_by": ["bam_rseqc"],
+                        "patch": "modules/nf-core/rseqc/tin/rseqc-tin.diff"
                     },
                     "salmon/index": {
                         "branch": "master",