Rearranging for clarity

[arvados-tutorial.git] / cwl / helper / gather-vcf.cwl

diff --git a/cwl/helper/gather-vcf.cwl b/cwl/helper/gather-vcf.cwl
deleted file mode 100644 (file)
index 8e5b29a..0000000
--- a/cwl/helper/gather-vcf.cwl
+++ /dev/null
@@ -1,57 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Gathering vcf using Picard 
-$namespaces:
-  arv: "http://arvados.org/cwl#"
-  cwltool: "http://commonwl.org/cwltool#"
-
-requirements:
-  DockerRequirement:
-    dockerPull: broadinstitute/gatk:4.1.7.0
-  ShellCommandRequirement: {}
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.gvcf1)
-      - $(inputs.gvcf2)
-
-hints:
-  ResourceRequirement:
-    ramMin: 20000
-    coresMin: 4    
-  arv:RuntimeConstraints:
-    outputDirType: keep_output_dir
-
-inputs:
-  gvcf1:
-    type: File
-  gvcf2:
-    type: File
-  sample: string
-  reference:
-    type: File
-    secondaryFiles:
-      - .amb
-      - .ann
-      - .bwt
-      - .pac
-      - .sa
-      - .fai
-      - ^.dict
-outputs:
-  gatheredgvcf:
-    type: File
-    outputBinding:
-      glob: "*.g.vcf.gz"
-
-baseCommand: /gatk/gatk
-
-arguments:
-  - "--java-options"
-  - "-Xmx8G" 
-  - GatherVcfs
-  - "-I"
-  - $(inputs.gvcf1.basename) 
-  - "-I"
-  - $(inputs.gvcf2.basename)
-  - prefix: "-O"
-    valueFrom: $(inputs.sample).g.vcf.gz