Rearranging for clarity

[arvados-tutorial.git] / cwl / helper / mark-duplicates.cwl

diff --git a/cwl/helper/mark-duplicates.cwl b/cwl/helper/mark-duplicates.cwl
deleted file mode 100644 (file)
index 3d7cba6..0000000
--- a/cwl/helper/mark-duplicates.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Marking Duplicates using Picard 
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
-  DockerRequirement:
-    dockerPull: broadinstitute/gatk:4.1.7.0
-
-hints:
-  ResourceRequirement:
-    ramMin: 20000
-    coresMin: 4    
-  arv:RuntimeConstraints:
-    outputDirType: keep_output_dir
-
-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"