Merge branch 'dev' into strand_param_fixes

nf-core · Jun 20, 2024 · b98095c · b98095c
2 parents 18f59c7 + 83e18b6
commit b98095c
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -80,6 +80,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes
 - [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison
 - [PR #1325](https://github.com/nf-core/rnaseq/pull/1325) - Minor fixes to strandedness settings and messaging
+- [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file
 
 ### Parameters
 

diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml
@@ -0,0 +1,15 @@
+name: deseq2_qc
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::r-base
+  - conda-forge::r-optparse
+  - conda-forge::r-ggplot2
+  - conda-forge::r-rcolorbrewer
+  - conda-forge::r-pheatmap
+  - bioconda::bioconductor-deseq2
+  - bioconda::bioconductor-biocparallel
+  - bioconda::bioconductor-tximport
+  - bioconda::bioconductor-complexheatmap
diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.nf
@@ -3,7 +3,7 @@ process DESEQ2_QC {
 
     // (Bio)conda packages have intentionally not been pinned to a specific version
     // This was to avoid the pipeline failing due to package conflicts whilst creating the environment when using -profile conda
-    conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' :
         'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }"

diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml
@@ -0,0 +1,7 @@
+name: gtf2bed
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::perl=5.26.2
diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf
@@ -2,7 +2,7 @@ process GTF2BED {
     tag "$gtf"
     label 'process_low'
 
-    conda "conda-forge::perl=5.26.2"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/perl:5.26.2' :
         'biocontainers/perl:5.26.2' }"

diff --git a/modules/local/gtf_filter/environment.yml b/modules/local/gtf_filter/environment.yml
@@ -0,0 +1,7 @@
+name: gtf_filter
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::python=3.9.5
diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf
@@ -1,7 +1,7 @@
 process GTF_FILTER {
     tag "$fasta"
 
-    conda "conda-forge::python=3.9.5"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'biocontainers/python:3.9--1' }"

diff --git a/modules/local/multiqc_custom_biotype/environment.yml b/modules/local/multiqc_custom_biotype/environment.yml
@@ -0,0 +1,7 @@
+name: multiqc_custom_biotype
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::python=3.9.5
diff --git a/modules/local/multiqc_custom_biotype/main.nf b/modules/local/multiqc_custom_biotype/main.nf
@@ -1,7 +1,7 @@
 process MULTIQC_CUSTOM_BIOTYPE {
     tag "$meta.id"
 
-    conda "conda-forge::python=3.9.5"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
         'biocontainers/python:3.9--1' }"

diff --git a/modules/local/preprocess_transcripts_fasta_gencode/environment.yml b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml
@@ -0,0 +1,7 @@
+name: preprocess_transcripts_fasta_gencode
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/local/preprocess_transcripts_fasta_gencode/main.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf
@@ -1,7 +1,7 @@
 process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE {
     tag "$fasta"
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"

diff --git a/modules/local/rsem_merge_counts/environment.yml b/modules/local/rsem_merge_counts/environment.yml
@@ -0,0 +1,7 @@
+name: rsem_merge_counts
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::sed=4.7
diff --git a/modules/local/rsem_merge_counts/main.nf b/modules/local/rsem_merge_counts/main.nf
@@ -1,7 +1,7 @@
 process RSEM_MERGE_COUNTS {
     label "process_medium"
 
-    conda "conda-forge::sed=4.7"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
         'nf-core/ubuntu:20.04' }"

diff --git a/modules/local/star_align_igenomes/environment.yml b/modules/local/star_align_igenomes/environment.yml
@@ -0,0 +1,9 @@
+name: star_align_igenomes
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::star=2.6.1d
+  - bioconda::samtools=1.10
+  - conda-forge::gawk=5.1.0
diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf
@@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"

diff --git a/modules/local/star_align_igenomes/tests/main.nf.test b/modules/local/star_align_igenomes/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process STAR_ALIGN_IGENOMES"
     script "../main.nf"
     process "STAR_ALIGN_IGENOMES"
-    tag "STAR_ALIGN_IGENOMES"
     tag "STAR_GENOMEGENERATE_IGENOMES"
 
     setup {

diff --git a/modules/local/star_genomegenerate_igenomes/environment.yml b/modules/local/star_genomegenerate_igenomes/environment.yml
@@ -0,0 +1,9 @@
+name: star_genomegenerate_igenomes
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::star=2.6.1d
+  - bioconda::samtools=1.10
+  - conda-forge::gawk=5.1.0
diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf
@@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES {
     tag "$fasta"
     label 'process_high'
 
-    conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' :
         'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }"