Merge branch 'develop' of github.com:msk-access/cwl_subworkflows into develop

Author: rhshah

gbcms_genotyping/gbcms_genotyping__packed.cwl

@@ -198,6 +198,9 @@
                 },
                 {
                     "class": "InlineJavascriptRequirement"
+                },
+                {
+                    "class": "StepInputExpressionRequirement"
                 }
             ],
             "http://purl.org/dc/terms/contributor": [

qc_collapsed_bam/qc_collapsed_bam.cwl

@@ -117,6 +117,10 @@ inputs:
     type: File
     'sbg:x': 0
     'sbg:y': 1893.34375
+  - id: bed_file
+    type: File?
+    'sbg:x': -5.7914533615112305
+    'sbg:y': 1468.1177978515625
 outputs:
   - id: fgbio_collect_duplex_seq_metrics_duplex_family_size_pool_a
     outputSource:
@@ -635,6 +639,8 @@ steps:
         source: reference
       - id: vcf_file
         source: vcf_file
+      - id: bed_file
+        source: bed_file
     out:
       - id: biometrics_extract_pickle
     run: ../command_line_tools/biometrics_extract/0.2.13/biometrics_extract.cwl
@@ -654,11 +660,11 @@ steps:
         default: 1
       - id: maf
         source: maf
-      - id: ref_fasta
-        source: reference
       - id: output
         source: sample_name
         valueFrom: $(self + '_collapsed_hotspots_fillout.maf')
+      - id: ref_fasta
+        source: reference
     out:
       - id: fillout
     run: >-
@@ -669,4 +675,3 @@ steps:
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: InlineJavascriptRequirement
-

qc_collapsed_bam/qc_collapsed_bam__packed.cwl

@@ -2475,6 +2475,9 @@
                 },
                 {
                     "class": "InlineJavascriptRequirement"
+                },
+                {
+                    "class": "StepInputExpressionRequirement"
                 }
             ],
             "http://purl.org/dc/terms/contributor": [
@@ -2721,6 +2724,15 @@
                     "type": "File",
                     "https://www.sevenbridges.com/x": 0,
                     "https://www.sevenbridges.com/y": 1893.34375
+                },
+                {
+                    "id": "#bed_file",
+                    "type": [
+                        "null",
+                        "File"
+                    ],
+                    "https://www.sevenbridges.com/x": -5.7914533615112305,
+                    "https://www.sevenbridges.com/y": 1468.1177978515625
                 }
             ],
             "outputs": [
@@ -3603,6 +3615,10 @@
                         {
                             "id": "#biometrics_extract_0_2_13/vcf_file",
                             "source": "#vcf_file"
+                        },
+                        {
+                            "id": "#biometrics_extract_0_2_13/bed_file",
+                            "source": "#bed_file"
                         }
                     ],
                     "out": [
@@ -3641,14 +3657,14 @@
                             "id": "#getbasecountsmultisample_1_2_5/maf",
                             "source": "#maf"
                         },
-                        {
-                            "id": "#getbasecountsmultisample_1_2_5/ref_fasta",
-                            "source": "#reference"
-                        },
                         {
                             "id": "#getbasecountsmultisample_1_2_5/output",
                             "source": "#sample_name",
                             "valueFrom": "$(self + '_collapsed_hotspots_fillout.maf')"
+                        },
+                        {
+                            "id": "#getbasecountsmultisample_1_2_5/ref_fasta",
+                            "source": "#reference"
                         }
                     ],
                     "out": [
@@ -3665,9 +3681,6 @@
             "requirements": [
                 {
                     "class": "SubworkflowFeatureRequirement"
-                },
-                {
-                    "class": "InlineJavascriptRequirement"
                 }
             ]
         }

qc_duplex_bam/qc_duplex_bam__packed.cwl

@@ -2046,6 +2046,9 @@
                 },
                 {
                     "class": "InlineJavascriptRequirement"
+                },
+                {
+                    "class": "StepInputExpressionRequirement"
                 }
             ],
             "http://purl.org/dc/terms/contributor": [