Merge pull request #1157 from maxulysse/vep_custom_args

Move all vep args from ext.args to params.vep_custom_args

Author: maxulysse

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#1151](https://github.com/nf-core/sarek/pull/1151) - Refactor codebase
+- [#1157](https://github.com/nf-core/sarek/pull/1157) - Move all vep args from `ext.args` to `params.vep_custom_args` to allow easier modifications
 
 ### Fixed
 

conf/modules/annotate.config

@@ -36,7 +36,6 @@ process {
     if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
         withName: 'ENSEMBLVEP_VEP' {
             ext.args         = { [
-                '--everything --filter_common --per_gene --total_length --offline --format vcf',
                 (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" : '',

nextflow.config

@@ -73,8 +73,8 @@ params {
     sentieon_haplotyper_emit_mode = "variant" // default value for Sentieon haplotyper
 
     // Annotation
-    vep_out_format      = 'vcf'
-    vep_custom_args     = null  // No custom arguments for VEP
+    vep_out_format      = "vcf"
+    vep_custom_args     = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
     vep_dbnsfp          = null  // dbnsfp plugin disabled within VEP
     dbnsfp              = null  // No dbnsfp processed file
     dbnsfp_tbi          = null  // No dbnsfp processed file index

nextflow_schema.json

@@ -487,6 +487,7 @@
                 },
                 "vep_custom_args": {
                     "type": "string",
+                    "default": "--everything --filter_common --per_gene --total_length --offline --format vcf",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Add an extra custom argument to VEP.",
                     "hidden": true,