Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+ - class: DockerRequirement
+ dockerPull: curii/clinvar-report
+ - class: ShellCommandRequirement
+
+hints:
+ ResourceRequirement:
+ ramMin: 10000
+ coresMin: 4
+
+stdout: $(inputs.vcf.nameroot).txt
+
+arguments:
+ - bcftools
+ - annotate
+ - prefix: "-a"
+ valueFrom: $(inputs.clinvarvcf.path)
+ - prefix: "-c"
+ valueFrom: "ID,INFO"
+ - $(inputs.vcf.path)
+ - {valueFrom: '|', shellQuote: false}
+ - bcftools
+ - filter
+ - prefix: "-i"
+ valueFrom: "INFO/ALLELEID>=1"
+
+inputs:
+ vcf:
+ type: File
+ clinvarvcf:
+ type: File
+
+outputs:
+ report: stdout
--- /dev/null
+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+ DockerRequirement:
+ dockerPull: curii/clinvar-report
+
+hints:
+ ResourceRequirement:
+ ramMin: 10000
+ coresMin: 4
+
+baseCommand: python
+
+arguments:
+ - $(inputs.reportfunc)
+ - $(inputs.sampletxt)
+ - $(inputs.sampletxt.basename)
+ - $(inputs.headhtml)
+ - $(inputs.tailhtml)
+
+inputs:
+ reportfunc:
+ type: File
+ sampletxt:
+ type: File
+ headhtml:
+ type: File
+ tailhtml:
+ type: File
+
+outputs:
+ report:
+ type: File
+ outputBinding:
+ glob: "*html"