ADD: new vep_custom_args

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#971](https://github.com/nf-core/sarek/pull/971) - Subtle bugfix to correct mutation of FASTP output channel objects
 - [#978](https://github.com/nf-core/sarek/pull/978) - Validate that patient/sample does not contain spaces
 - [#981](https://github.com/nf-core/sarek/pull/981) - Added documentation on generating ASCAT resources for exome and targeted sequencing
+- [#1041](https://github.com/nf-core/sarek/pull/1041) - Add params `vep_custom_args` to let user specify custom params more easily for `VEP`
 
 ### Changed
 

conf/modules/annotate.config

@@ -42,7 +42,8 @@ process {
                 (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_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)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf'
+                (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf',
+                (params.vep_custom_args)                                              ?: ''
             ].join(' ').trim() }
             // If just VEP: <vcf prefix>_VEP.ann.vcf
             ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP.ann" }

nextflow.config

@@ -72,6 +72,7 @@ params {
 
     // Annotation
     vep_out_format      = 'vcf'
+    vep_custom_args     = ''    // No custom 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

@@ -473,6 +473,13 @@
                     "hidden": true,
                     "help_text": "For details, see [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#spliceregion) and [here](https://www.ensembl.info/2018/10/26/cool-stuff-the-vep-can-do-splice-site-variant-annotation/)."
                 },
+                "vep_custom_args": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-toolbox",
+                    "description": "Add an extra custom argument to VEP.",
+                    "hidden": true,
+                    "help_text": "Using this params you can add custom args to VEP."
+                },
                 "snpeff_cache": {
                     "type": "string",
                     "fa_icon": "fas fa-file",
@@ -489,13 +496,15 @@
                 },
                 "outdir_cache": {
                     "type": "string",
+                    "fa_icon": "fas fa-file",
                     "format": "directory-path",
                     "description": "The output directory where the cache will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open",
                     "hidden": true
                 },
                 "vep_out_format": {
                     "type": "string",
+                    "fa_icon": "fas fa-file",
                     "default": "vcf",
                     "description": "VEP output-file format.",
                     "enum": ["json", "tab", "vcf"],