updating cwl

[arvados-tutorial.git] / cwl / calc-coverage.cwl

diff --git a/cwl/calc-coverage.cwl b/cwl/calc-coverage.cwl
new file mode 100644 (file)
index 0000000..b1e9373
--- /dev/null
+++ b/cwl/calc-coverage.cwl
@@ -0,0 +1,39 @@
+cwlVersion: v1.1
+class: CommandLineTool
+label: Marking Duplicates using Picard 
+
+requirements:
+  DockerRequirement:
+    dockerPull: broadinstitute/gatk
+
+hints:
+  ResourceRequirement:
+    ramMin: 20000
+    coresMin: 4    
+
+inputs:
+  bam:
+    type: File
+
+outputs:
+  dupbam:
+    type: File
+    outputBinding:
+      glob: "*.bam"
+  dupmetrics:
+    type: File
+    outputBinding:
+      glob: "*.txt"
+
+baseCommand: /gatk/gatk
+
+arguments:
+  - "--java-options"
+  - "-Xmx8G" 
+  - MarkDuplicates
+  - prefix: "-I"
+    valueFrom: $(inputs.bam.path)
+  - prefix: "-O"
+    valueFrom: marked_dups$(inputs.bam.basename)
+  - prefix: "-M"
+    valueFrom: "metrics.txt"