Merge pull request #194 from msk-access/write_opFiles

Author: rhshah

vardict_workflow/run_processed_vardict.cwl

@@ -59,6 +59,24 @@ outputs:
     type: File
     'sbg:x': 1064.255126953125
     'sbg:y': 213.53125
+  - id: vardict_output
+    outputSource:
+      - vardict/output
+    type: File
+    'sbg:x': 397.9921875
+    'sbg:y': 590.5
+  - id: single_filter_vcf
+    outputSource:
+      - pv_vardict_single_filter/vcf
+    type: File
+    'sbg:x': 688.9921875
+    'sbg:y': 587.5
+  - id: single_filter_vcf_complex
+    outputSource:
+      - pv_vardict_single_filter/vcf_complex
+    type: File
+    'sbg:x': 942.9921875
+    'sbg:y': 552.5
 steps:
   - id: vardict
     in:
@@ -113,8 +131,8 @@ steps:
       - id: vcf
     run: >-
       ../command_line_tools/postprocessing_variant_calls/0.1.5/pv_vardict_single_filter.cwl
-    'sbg:x': 513.37158203125
-    'sbg:y': 213.53125
+    'sbg:x': 483
+    'sbg:y': 220
   - id: variants_concat
     in:
       - id: fastaRef

vardict_workflow/run_processed_vardict__packed.cwl

@@ -1731,6 +1731,33 @@
                     "type": "File",
                     "https://www.sevenbridges.com/x": 1064.255126953125,
                     "https://www.sevenbridges.com/y": 213.53125
+                },
+                {
+                    "id": "#main/vardict_output",
+                    "outputSource": [
+                        "#main/vardict/output"
+                    ],
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 397.9921875,
+                    "https://www.sevenbridges.com/y": 590.5
+                },
+                {
+                    "id": "#main/single_filter_vcf",
+                    "outputSource": [
+                        "#main/pv_vardict_single_filter/vcf"
+                    ],
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 688.9921875,
+                    "https://www.sevenbridges.com/y": 587.5
+                },
+                {
+                    "id": "#main/single_filter_vcf_complex",
+                    "outputSource": [
+                        "#main/pv_vardict_single_filter/vcf_complex"
+                    ],
+                    "type": "File",
+                    "https://www.sevenbridges.com/x": 942.9921875,
+                    "https://www.sevenbridges.com/y": 552.5
                 }
             ],
             "steps": [
@@ -1837,8 +1864,8 @@
                         }
                     ],
                     "run": "#pv_vardict_single_filter.cwl",
-                    "https://www.sevenbridges.com/x": 513.37158203125,
-                    "https://www.sevenbridges.com/y": 213.53125
+                    "https://www.sevenbridges.com/x": 483,
+                    "https://www.sevenbridges.com/y": 220
                 },
                 {
                     "id": "#main/variants_concat",

variant_annotation/variant_annotation.cwl

@@ -105,14 +105,20 @@ outputs:
     outputSource:
       - maf_annotated_by_bed_mappability/output
     type: File
-    'sbg:x': 1448.455810546875
-    'sbg:y': 54.44126510620117
+    'sbg:x': 1524.598876953125
+    'sbg:y': 679.8934936523438
   - id: output_complexity_maf
     outputSource:
       - maf_annotated_by_bed_lowComplexity/output
     type: File
     'sbg:x': 1815.8809814453125
     'sbg:y': 248.1118621826172
+  - id: oncokb_maf
+    outputSource:
+      - oncokb_annotator/outputMaf
+    type: File?
+    'sbg:x': 1327.9454345703125
+    'sbg:y': 738.3821411132812
 steps:
   - id: snpsift_annotate_5_0
     in:

variant_annotation/variant_annotation__packed.cwl

@@ -1006,8 +1006,8 @@
                         "#main/maf_annotated_by_bed_mappability/output"
                     ],
                     "type": "File",
-                    "https://www.sevenbridges.com/x": 1448.455810546875,
-                    "https://www.sevenbridges.com/y": 54.44126510620117
+                    "https://www.sevenbridges.com/x": 1524.598876953125,
+                    "https://www.sevenbridges.com/y": 679.8934936523438
                 },
                 {
                     "id": "#main/output_complexity_maf",
@@ -1017,6 +1017,18 @@
                     "type": "File",
                     "https://www.sevenbridges.com/x": 1815.8809814453125,
                     "https://www.sevenbridges.com/y": 248.1118621826172
+                },
+                {
+                    "id": "#main/oncokb_maf",
+                    "outputSource": [
+                        "#main/oncokb_annotator/outputMaf"
+                    ],
+                    "type": [
+                        "null",
+                        "File"
+                    ],
+                    "https://www.sevenbridges.com/x": 1327.9454345703125,
+                    "https://www.sevenbridges.com/y": 738.3821411132812
                 }
             ],
             "steps": [