Adding cwl to convert gvcf to vcf

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

diff --git a/cwl/gvcf-to-vcf.cwl b/cwl/gvcf-to-vcf.cwl
new file mode 100644 (file)
index 0000000..ecba357
--- /dev/null
+++ b/cwl/gvcf-to-vcf.cwl
@@ -0,0 +1,42 @@
+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)
+  - 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