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update local modules #1311

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merged 2 commits into from
Nov 3, 2023
Merged

update local modules #1311

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736fbe8
update local moduels
maxulysse Nov 3, 2023
9d6bd9b
update CHANGELOG
maxulysse Nov 3, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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6 changes: 6 additions & 0 deletions modules/local/add_info_to_vcf/environment.yml
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@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- anaconda::gawk=5.1.0
2 changes: 1 addition & 1 deletion modules/local/add_info_to_vcf/main.nf
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Expand Up @@ -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' }"
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6 changes: 6 additions & 0 deletions modules/local/build_intervals/environment.yml
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@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- anaconda::gawk=5.1.0
2 changes: 1 addition & 1 deletion modules/local/build_intervals/main.nf
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Expand Up @@ -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' }"
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6 changes: 6 additions & 0 deletions modules/local/create_intervals_bed/environment.yml
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@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- anaconda::gawk=5.1.0
2 changes: 1 addition & 1 deletion modules/local/create_intervals_bed/main.nf
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Expand Up @@ -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' }"
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