adding helper directory for structure, may reorg later

[arvados-tutorial.git] / cwl / gvcf-to-vcf.cwl

diff --git a/cwl/gvcf-to-vcf.cwl b/cwl/gvcf-to-vcf.cwl
deleted file mode 100644 (file)
index dfa3e24..0000000
--- a/cwl/gvcf-to-vcf.cwl
+++ /dev/null
@@ -1,44 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-label: Converts gvcf to vcf
-
-requirements:
-  - class: DockerRequirement
-    dockerPull: curii/clinvar-report
-  - class: ShellCommandRequirement
-
-hints:
-  ResourceRequirement:
-    ramMin: 10000
-    coresMin: 4
-
-inputs:
-  samplename:
-    type: string
-  gvcf:
-    type: File
-  
-outputs:
-  vcf:
-    type: File
-    outputBinding:
-      glob: "*.vcf.gz"
-    secondaryFiles: [.tbi]
-
-arguments:
-  - bcftools
-  - view 
-  - prefix: "--min-ac"
-    valueFrom: "1"
-  - $(inputs.gvcf.path)
-  - prefix: "-i"
-    valueFrom: "AVG(GQ)>20"
-  - valueFrom: "-Ov"
-  - prefix: "-o"
-    valueFrom: $(inputs.samplename).vcf
-  - {valueFrom: '&&', shellQuote: false}
-  - bgzip
-  - valueFrom: $(inputs.samplename).vcf
-  - {valueFrom: '&&', shellQuote: false}
-  - tabix
-  - valueFrom: $(inputs.samplename).vcf.gz