Merge pull request #192 from msk-access/vep_path

adding VEP path and data as default

Author: rhshah

variant_annotation/variant_annotation.cwl

@@ -158,6 +158,10 @@ steps:
         source: tumor_id
       - id: vcf_tumor_id
         source: tumor_id
+      - id: vep_data
+        default: /.vep/
+      - id: vep_path
+        default: /usr/local/bin/
     out:
       - id: vcf2maf_maf
     run: ../command_line_tools//vcf2maf_1.6.21/vcf2maf_1.6.21.cwl

variant_annotation/variant_annotation__packed.cwl

@@ -1102,6 +1102,14 @@
                         {
                             "id": "#main/vcf2maf_v1_6_21/vcf_tumor_id",
                             "source": "#main/tumor_id"
+                        },
+                        {
+                            "id": "#main/vcf2maf_v1_6_21/vep_data",
+                            "default": "/.vep/"
+                        },
+                        {
+                            "id": "#main/vcf2maf_v1_6_21/vep_path",
+                            "default": "/usr/local/bin/"
                         }
                     ],
                     "out": [