Merge pull request #1311 from maxulysse/local_modules

update local modules
nf-core · Nov 3, 2023 · a1355ea · a1355ea
2 parents d6a1230 + 9d6bd9b
commit a1355ea
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3
 - [#1303](https://github.com/nf-core/sarek/pull/1303) - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin
 - [#1304](https://github.com/nf-core/sarek/pull/1304) - Update modules
+- [#1311](https://github.com/nf-core/sarek/pull/1311) - Update local modules with an `environment.yml` file
 
 ### Fixed
 

diff --git a/modules/local/add_info_to_vcf/environment.yml b/modules/local/add_info_to_vcf/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - anaconda::gawk=5.1.0
diff --git a/modules/local/add_info_to_vcf/main.nf b/modules/local/add_info_to_vcf/main.nf
@@ -2,7 +2,7 @@ process ADD_INFO_TO_VCF {
     tag "$meta.id"
     label 'process_single'
 
-    conda "anaconda::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
         'biocontainers/gawk:5.1.0' }"

diff --git a/modules/local/build_intervals/environment.yml b/modules/local/build_intervals/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - anaconda::gawk=5.1.0
diff --git a/modules/local/build_intervals/main.nf b/modules/local/build_intervals/main.nf
@@ -2,7 +2,7 @@ process BUILD_INTERVALS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "anaconda::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
         'biocontainers/gawk:5.1.0' }"

diff --git a/modules/local/create_intervals_bed/environment.yml b/modules/local/create_intervals_bed/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - anaconda::gawk=5.1.0
diff --git a/modules/local/create_intervals_bed/main.nf b/modules/local/create_intervals_bed/main.nf
@@ -2,7 +2,7 @@ process CREATE_INTERVALS_BED {
     tag "$intervals"
     label 'process_single'
 
-    conda "anaconda::gawk=5.1.0"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
         'biocontainers/gawk:5.1.0' }"