Merge pull request #582 from asp8200/vep_output_format

Adding option for setting file-output-format for VEP

Author: maxulysse

CHANGELOG.md

@@ -29,6 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#540](https://github.com/nf-core/sarek/pull/540) - Add modules and subworkflows for `cnvkit` somatic mode
 - [#557](https://github.com/nf-core/sarek/pull/557) - Add `Haplotypecaller` single sample mode together with `CNNScoreVariants` and `FilterVariantTranches`
 - [#576](https://github.com/nf-core/sarek/pull/576) - Add modules and subworkflows for `cnvkit` germline mode
+- [#582](https://github.com/nf-core/sarek/pull/582) - Added option `--vep_out_format` for setting the format of the output-file from VEP to `json`, `tab` or `vcf` (default)
 
 ### Changed
 

conf/modules.config

@@ -1056,18 +1056,30 @@ process{
             (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_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.${params.genome}" }
         publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/EnsemblVEP/${meta.id}/${meta.variantcaller}" },
-            pattern: "*html"
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/reports/EnsemblVEP/${meta.id}/${meta.variantcaller}" },
+                pattern: "*html"
+            ],
+            [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/annotation/${meta.id}/${meta.variantcaller}" },
+                pattern: "*{json,tab}"
+            ]
         ]
     }
 
+    withName: 'NFCORE_SAREK:SAREK:ANNOTATE:ANNOTATION_ENSEMBLVEP:ENSEMBLVEP' {
+        ext.prefix      = {"${meta.id}_VEP"}
+    }
+
     withName: ".*:ANNOTATION_MERGE:ENSEMBLVEP" {
-        // Output file will have format *_snpEff_VEP.ann.vcf
+        // Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
         ext.prefix       = { "${vcf.baseName.minus(".ann.vcf")}_VEP" }
     }
 

modules.json

@@ -67,7 +67,7 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "ensemblvep": {
-                "git_sha": "40dd662fd26c3eb3160b7c8cbbe9bff80bbe2c30"
+                "git_sha": "30f72e24822576c6f90a0bf9db678b403c70eccf"
             },
             "fastqc": {
                 "git_sha": "49b18b1639f4f7104187058866a8fab33332bdfe"

modules/nf-core/modules/ensemblvep/Dockerfile

@@ -67,6 +67,7 @@ params {
 
 
     // Annotation
+    vep_out_format = 'vcf'
     vep_dbnsfp = null // dbnsfp plugin disabled within VEP
     dbnsfp = null // No dbnsfp processed file
     dbnsfp_tbi = null // No dbnsfp processed file index

modules/nf-core/modules/ensemblvep/build.sh

@@ -538,6 +538,14 @@
                     "description": "VEP cache version.",
                     "help_text": "If you use AWS iGenomes, this has already been set for you appropriately."
                 },
+                "vep_out_format": {
+                    "type": "string",
+                    "default": "vcf",
+                    "description": "VEP output-file format.",
+                    "enum": ["json", "tab", "vcf"],
+                    "help_text": "Sets the format of the output-file from VEP. Available formats: json, tab and vcf.",
+                    "fa_icon": "fas fa-table"
+                },
                 "save_reference": {
                     "type": "boolean",
                     "fa_icon": "fas fa-download",