adding normal_id as an input

mskcc · Jul 22, 2024 · 5566a5a · 5566a5a
1 parent 1f48278
commit 5566a5a
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Showing 3 changed files with 19 additions and 11 deletions.
diff --git a/Goliath b/Goliath
diff --git a/cwl/project_level_report.cwl b/cwl/project_level_report.cwl
@@ -10,12 +10,14 @@ requirements:
   StepInputExpressionRequirement: {}
   InlineJavascriptRequirement: {}
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.6
+    dockerPull: mskcc/argos_report:dev
 
 inputs:
   request_id:
     type: string
-  sample_ids:
+  tumor_ids:
+    type: string[]
+  normal_ids:
     type: string[]
   portal_dir:
     type: Directory
@@ -29,12 +31,13 @@ steps:
     run: report.cwl
     in:
       request_id: request_id
-      sample_id: sample_ids
+      tumor_id: tumor_ids
+      normal_id: normal_ids
       portal_dir: portal_dir
       analysis_dir: analysis_dir
       oncokb_file: oncokb_file
 
-    scatter: sample_id
+    scatter: [tumor_id, normal_id]
     scatterMethod: dotproduct
     out: [output_file]
 

diff --git a/cwl/report.cwl b/cwl/report.cwl
@@ -5,33 +5,38 @@ class: CommandLineTool
 baseCommand: [ "compile_sample_level.R" ]
 requirements:
   DockerRequirement:
-    dockerPull: mskcc/argos_report:1.0.6
+    dockerPull: mskcc/argos_report:dev
 
 inputs:
   request_id:
     type: string
     inputBinding:
       position: 1
       prefix: '--request_id'
-  sample_id:
+  tumor_id:
     type: string
     inputBinding:
       position: 2
-      prefix: '--sample_id'
+      prefix: '--tumor_id'
+  normal_id:
+    type: string
+    inputBinding:
+      position: 3
+      prefix: '--normal_id'
   portal_dir:
     type: Directory
     inputBinding:
-      position: 3
+      position: 4
       prefix: '--portal_dir'
   analysis_dir:
     type: Directory
     inputBinding:
-      position: 4
+      position: 5
       prefix: '--analysis_dir'
   oncokb_file:
       type: File
       inputBinding:
-        position: 5
+        position: 6
         prefix: '--oncokb_file'