Merge branch 'dev' into prerelease_3.14.0_fixes

nf-core · Jan 4, 2024 · fbb50ce · fbb50ce
2 parents 7843299 + 63df1d7
commit fbb50ce
Show file tree

Hide file tree

Showing 21 changed files with 232 additions and 37 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,6 +25,8 @@ Special thanks to the following for their contributions to the release:
 - [PR #1144](https://github.com/nf-core/rnaseq/pull/1144) - Interface to kmer size for pseudoaligners ([#1111](https://github.com/nf-core/rnaseq/issues/1111))
 - [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))
 - [PR #1154](https://github.com/nf-core/rnaseq/pull/1154) - Prerelease 3.14.0 fixes ([#1111](https://github.com/nf-core/rnaseq/issues/1111), [#1153](https://github.com/nf-core/rnaseq/issues/1153))
 
 ### Parameters
@@ -37,6 +39,19 @@ 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

diff --git a/bin/tx2gene.py b/bin/tx2gene.py
@@ -62,7 +62,7 @@ def discover_transcript_attribute(gtf_file: str, transcripts: Set[str]) -> str:
             attributes_str = cols[8]
             attributes = dict(re.findall(r'(\S+) "(.*?)(?<!\\)";', attributes_str))
 
-            votes.update(key for key, value in attributes.items())
+            votes.update(key for key, value in attributes.items() if value in transcripts)
 
     if not votes:
         # Log a warning if no matching attribute is found

diff --git a/modules.json b/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",

diff --git a/modules/nf-core/qualimap/rnaseq/main.nf b/modules/nf-core/qualimap/rnaseq/main.nf
diff --git a/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff b/modules/nf-core/qualimap/rnaseq/qualimap-rnaseq.diff
diff --git a/modules/nf-core/rseqc/bamstat/main.nf b/modules/nf-core/rseqc/bamstat/main.nf
diff --git a/modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff b/modules/nf-core/rseqc/bamstat/rseqc-bamstat.diff
diff --git a/modules/nf-core/rseqc/inferexperiment/main.nf b/modules/nf-core/rseqc/inferexperiment/main.nf
diff --git a/modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff b/modules/nf-core/rseqc/inferexperiment/rseqc-inferexperiment.diff
diff --git a/modules/nf-core/rseqc/innerdistance/main.nf b/modules/nf-core/rseqc/innerdistance/main.nf
diff --git a/modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff b/modules/nf-core/rseqc/innerdistance/rseqc-innerdistance.diff
diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf
diff --git a/modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff b/modules/nf-core/rseqc/junctionannotation/rseqc-junctionannotation.diff
diff --git a/modules/nf-core/rseqc/junctionsaturation/main.nf b/modules/nf-core/rseqc/junctionsaturation/main.nf
diff --git a/modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff b/modules/nf-core/rseqc/junctionsaturation/rseqc-junctionsaturation.diff
diff --git a/modules/nf-core/rseqc/readdistribution/main.nf b/modules/nf-core/rseqc/readdistribution/main.nf
diff --git a/modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff b/modules/nf-core/rseqc/readdistribution/rseqc-readdistribution.diff
diff --git a/modules/nf-core/rseqc/readduplication/main.nf b/modules/nf-core/rseqc/readduplication/main.nf
diff --git a/modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff b/modules/nf-core/rseqc/readduplication/rseqc-readduplication.diff
diff --git a/modules/nf-core/rseqc/tin/main.nf b/modules/nf-core/rseqc/tin/main.nf