Rearranging for clarity

[arvados-tutorial.git] / cwl / helper / not-in-use / check-sam.cwl

diff --git a/cwl/helper/not-in-use/check-sam.cwl b/cwl/helper/not-in-use/check-sam.cwl
deleted file mode 100644 (file)
index df15439..0000000
--- a/cwl/helper/not-in-use/check-sam.cwl
+++ /dev/null
@@ -1,51 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Validate Sam using Picard 
-
-requirements:
-  DockerRequirement:
-    dockerPull: broadinstitute/gatk
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.sam)
-
-hints:
-  ResourceRequirement:
-    ramMin: 20000
-    coresMin: 4    
-
-inputs:
-  sam:
-    type: File
-
-  reference:
-    type: File
-    secondaryFiles:
-      - .amb
-      - .ann
-      - .bwt
-      - .pac
-      - .sa
-      - .fai
-      - ^.dict
-
-outputs:
-  metrics:
-    type: File
-    outputBinding:
-      glob: "*.txt"
-
-baseCommand: /gatk/gatk
-
-arguments:
-  - "--java-options"
-  - "-Xmx8G" 
-  - ValidateSamFile 
-  - prefix: "-I"
-    valueFrom: $(inputs.sam.basename)
-  - prefix: "-M"
-    valueFrom: "SUMMARY"
-  - prefix: "-O"
-    valueFrom: "metrics.txt" 
-  - prefix: "-R"
-    valueFrom: $(inputs.reference.path)