8000 FEAT: Proper usage of vep_version by maxulysse · Pull Request #1303 · nf-core/sarek · GitHub
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FEAT: Proper usage of vep_version #1303

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Merged
merged 1 commit into from
Nov 1, 2023
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FEAT: Proper usage of vep_version #1303

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers
- [#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

### Fixed

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2 changes: 1 addition & 1 deletion conf/modules/annotate.config
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Expand Up @@ -37,7 +37,7 @@ process {
ext.args = { [
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path://usr/local/share/ensembl-vep-${params.vep_version}" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -95,6 +95,7 @@ params {
vep_out_format = "vcf"
vep_spliceai = null // spliceai plugin disabled within VEP
vep_spliceregion = null // spliceregion plugin disabled within VEP
vep_version = "110.0-0" // Should be updated when we update VEP, needs this to get full path to some plugins
bcftools_annotations = null // No extra annotation file
bcftools_annotations_index = null // No extra annotation file index
bcftools_header_lines = null // No header lines to be added to the VCF file
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7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -540,6 +540,13 @@
"description": "Add an extra custom argument to VEP.",
"help_text": "Using this params you can add custom args to VEP."
},
"vep_version": {
"type": "string",
"default": "110.0-0",
"fa_icon": "fas fa-toolbox",
"description": "Should reflect the VEP version used in the container.",
"help_text": "Used by the loftee plugin that need the full path."
},
"use_annotation_cache_keys": {
"type": "boolean",
"fa_icon": "fas fa-toolbox",
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