Merge branch 'dev' of https://github.com/nf-core/rnafusion into gener…

…al_fixes
nf-core · Nov 28, 2024 · 3058f0c · 3058f0c
2 parents eece50d + 3029fdf
commit 3058f0c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,13 +10,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Normalized gene expression calculated [#488](https://github.com/nf-core/rnafusion/pull/488)
 - Primary assembly now used as main reference genome FASTA file, as recommended by the STAR manual [#488](https://github.com/nf-core/rnafusion/pull/488)
 - Use of only ensembl GTF file, not chr.gtf file as GTF reference file [#488](https://github.com/nf-core/rnafusion/pull/488)
-- Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#508](https://github.com/nf-core/rnafusion/pull/508)
-- Add nf-test to local module: `HGNC_DOWNLOAD` [#508](https://github.com/nf-core/rnafusion/pull/509)
+- Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#539](https://github.com/nf-core/rnafusion/pull/539)
+- Add nf-test to local module: `HGNC_DOWNLOAD` [#540](https://github.com/nf-core/rnafusion/pull/540)
+- Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551)
 
 ### Changed
 
 - Updated modules and migrated non-specific modules to nf-core/modules [#484](https://github.com/nf-core/rnafusion/pull/484)
 - Updated to nf-core/tools 3.0.2 [#504](https://github.com/nf-core/rnafusion/pull/504)
+- Remove local module `RRNA_TRANSCRIPTS` (replaced by nf-core module) [#541](https://github.com/nf-core/rnafusion/pull/541)
 
 ### Fixed
 

diff --git a/modules.json b/modules.json
@@ -77,7 +77,7 @@
                     },
                     "picard/collectrnaseqmetrics": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "picard/collectwgsmetrics": {

diff --git a/modules/local/rrnatranscripts/main.nf b/modules/local/rrnatranscripts/main.nf
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config b/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config