diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b11cbe4e8..3133b0d2df 100644 --- 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 new file mode 100644 index 0000000000..710fbfd120 --- /dev/null +++ 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 index f36eb20062..a55cf14b56 100644 --- 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gawk:5.1.0' : 'biocontainers/gawk:5.1.0' }" diff --git a/modules/local/build_intervals/environment.yml b/modules/local/build_intervals/environment.yml new file mode 100644 index 0000000000..710fbfd120 --- /dev/null +++ b/modules/local/build_intervals/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - anaconda::gawk=5.1.0 diff --git a/modules/local/build_intervals/main.nf b/modules/local/build_intervals/main.nf index 8f8f0df23e..9c562f5c17 100644 --- a/modules/local/build_intervals/main.nf +++ b/modules/local/build_intervals/main.nf @@ -2,7 +2,7 @@ process BUILD_INTERVALS { tag "$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 new file mode 100644 index 0000000000..710fbfd120 --- /dev/null +++ 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 index 26c2689346..88160ccbf4 100644 --- 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' }"