Merge branch 'dev' into rnaseq_propro_trimfail_fix

nf-core · Sep 16, 2024 · 8244d50 · 8244d50
2 parents 5c6982c + 087a3a7
commit 8244d50
Show file tree

Hide file tree

Showing 67 changed files with 247 additions and 222 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,15 +5,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v3.16.0dev - [date]
 
-- [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
-
 ### Credits
 
 Special thanks to the following for their contributions to the release:
 
 ### 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
+
 ## [[3.15.0](https://github.com/nf-core/rnaseq/releases/tag/3.15.0)] - 2024-09-04
 
 ### Credits

diff --git a/modules.json b/modules.json
diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml
@@ -1,8 +1,6 @@
-name: deseq2_qc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::r-base
   - conda-forge::r-optparse

diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml
@@ -1,7 +1,5 @@
-name: gtf2bed
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::perl=5.26.2
diff --git a/modules/local/gtf_filter/environment.yml b/modules/local/gtf_filter/environment.yml
@@ -1,7 +1,5 @@
-name: gtf_filter
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::python=3.9.5
diff --git a/modules/local/multiqc_custom_biotype/environment.yml b/modules/local/multiqc_custom_biotype/environment.yml
@@ -1,7 +1,5 @@
-name: multiqc_custom_biotype
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::python=3.9.5
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/environment.yml b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml
@@ -1,7 +1,5 @@
-name: preprocess_transcripts_fasta_gencode
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::sed=4.7
diff --git a/modules/local/rsem_merge_counts/environment.yml b/modules/local/rsem_merge_counts/environment.yml
@@ -1,7 +1,5 @@
-name: rsem_merge_counts
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::sed=4.7
diff --git a/modules/local/star_align_igenomes/environment.yml b/modules/local/star_align_igenomes/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

diff --git a/modules/local/star_genomegenerate_igenomes/environment.yml b/modules/local/star_genomegenerate_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

diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml
diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml
diff --git a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py
diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml
diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml
diff --git a/modules/nf-core/custom/tx2gene/templates/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py
diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml
diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml
diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf
diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml
diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf