Merge pull request #1384 from nf-core/dev

Dev -> Master for 3.15.1

Author: pinin4fjords

CHANGELOG.md

@@ -3,6 +3,16 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[3.15.1](https://github.com/nf-core/rnaseq/releases/tag/3.15.1)] - 2024-09-16
+
+### Enhancements & fixes
+
+- [PR #1374](https://github.com/nf-core/rnaseq/pull/1374) - Bump pipeline version to 3.16.0dev
+- [PR #1380](https://github.com/nf-core/rnaseq/pull/1380) - Fix issues with R modules changing sample names
+- [PR #1381](https://github.com/nf-core/rnaseq/pull/1381) - Update all modules following massive conda usage update in nf-core modules
+- [PR #1382](https://github.com/nf-core/rnaseq/pull/1381) - Slight fixes for rnaseq preprocessing
+- [P$ #1383](https://github.com/nf-core/rnaseq/pull/1383) - Prerelease 3.15.1 version bumps
+
 ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04
 
 ### Credits

modules.json

@@ -1,8 +1,6 @@
-name: deseq2_qc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::r-base
   - conda-forge::r-optparse

modules/local/deseq2_qc/environment.yml

@@ -1,7 +1,5 @@
-name: gtf2bed
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::perl=5.26.2

modules/local/gtf2bed/environment.yml

@@ -1,7 +1,5 @@
-name: gtf_filter
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::python=3.9.5

modules/local/gtf_filter/environment.yml

@@ -1,7 +1,5 @@
-name: multiqc_custom_biotype
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::python=3.9.5

modules/local/multiqc_custom_biotype/environment.yml

@@ -1,7 +1,5 @@
-name: preprocess_transcripts_fasta_gencode
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::sed=4.7

modules/local/preprocess_transcripts_fasta_gencode/environment.yml

@@ -1,7 +1,5 @@
-name: rsem_merge_counts
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::sed=4.7

modules/local/rsem_merge_counts/environment.yml

@@ -1,8 +1,6 @@
-name: star_align_igenomes
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::star=2.6.1d
   - bioconda::samtools=1.10

modules/local/star_align_igenomes/environment.yml

@@ -1,8 +1,6 @@
-name: star_genomegenerate_igenomes
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::star=2.6.1d
   - bioconda::samtools=1.10