add params for dbnsfp vep plugin + fix filenames for vep plugins

CHANGELOG.md

@@ -34,6 +34,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#597](https://github.com/nf-core/sarek/pull/597) - Added tiddit for tumor variant calling
 - [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema
 - [#604](https://github.com/nf-core/sarek/pull/604) - Added full size tests WGS 30x NA12878
+- [#613](https://github.com/nf-core/sarek/pull/613) - Added params `--dbnsfp_fields` to allow configuration of fields for the `dbnsfp` `VEP` plugin
+- [#613](https://github.com/nf-core/sarek/pull/613) - Added params `--dbnsfp_consequence` to allow configuration of consequence for the `dbnsfp` `VEP` plugin
 
 ### Changed
 
@@ -107,6 +109,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#600](https://github.com/nf-core/sarek/pull/600) - Remove `nf-core lint` warnings
 - [#602](https://github.com/nf-core/sarek/pull/602) - Fixed bug in `alignment_to_fastq` and added tests
 - [#609](https://github.com/nf-core/sarek/pull/609) - Remove unused intervals code, reorganize combined intervals file
+- [#613](https://github.com/nf-core/sarek/pull/613) - Fixed filenames for  `dbnsfp` and `SpliceAI` `VEP` plugin
 
 ### Deprecated
 

conf/modules.config

@@ -1151,11 +1151,12 @@ process{
             ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP" }
             ext.args          = [
                 '--everything --filter_common --per_gene --total_length --offline --format vcf',
-                (params.vep_dbnsfp && params.dbnsfp)                                  ? '--plugin dbNSFP,dbNSFP.gz,rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF' : '',
-                (params.vep_loftee)                                                   ? '--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-104.3/share/ensembl-vep-104.3-0'                                      : '',
-                (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? '--plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz'                     : '',
-                (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                     : '',
-                (params.vep_out_format)                                               ? "--${params.vep_out_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,'${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
+                (params.vep_loftee)                                                   ? '--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-104.3/share/ensembl-vep-104.3-0'                   : '',
+                (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},${params.spliceai_indel.split("/")[-1]}"    : '',
+                (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                  : '',
+                (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                             : '--vcf'
             ].join(' ').trim()
             if (!params.vep_cache)    container = { params.vep_genome ? "nfcore/vep:104.3.${params.vep_genome}" : "nfcore/vep:104.3.${params.genome}" }
             publishDir       = [

nextflow.config

@@ -72,6 +72,8 @@ params {
     vep_dbnsfp = null // dbnsfp plugin disabled within VEP
     dbnsfp = null // No dbnsfp processed file
     dbnsfp_tbi = null // No dbnsfp processed file index
+    dbnsfp_consequence = null // No default consequence for dbnsfp plugin
+    dbnsfp_fields = "rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF" // Default fields for dbnsfp plugin
     vep_loftee = null // loftee plugin disabled within VEP
     vep_spliceai = null // spliceai plugin disabled within VEP
     spliceai_snv = null // No spliceai_snv file

nextflow_schema.json

@@ -335,6 +335,20 @@
                     "help_text": "To be used with `--vep_dbnsfp`.",
                     "hidden": true
                 },
+                "dbnsfp_consequence": {
+                    "type": "string",
+                    "fa_icon": "fas fa-database",
+                    "description": "Consequence to annotate with",
+                    "help_text": "To be used with `--vep_dbnsfp`.",
+                    "hidden": true
+                },
+                "dbnsfp_fields": {
+                    "type": "string",
+                    "fa_icon": "fas fa-database",
+                    "description": "Fields to annotate with",
+                    "help_text": "To be used with `--vep_dbnsfp`.",
+                    "hidden": true
+                },
                 "vep_loftee": {
                     "type": "boolean",
                     "fa_icon": "fas fa-database",