Rearranging for clarity

[arvados-tutorial.git] / WGS-processing / cwl / helper / annotate-vcf.cwl

diff --git a/WGS-processing/cwl/helper/annotate-vcf.cwl b/WGS-processing/cwl/helper/annotate-vcf.cwl
new file mode 100644 (file)
index 0000000..019fa1a
--- /dev/null
+++ b/WGS-processing/cwl/helper/annotate-vcf.cwl
@@ -0,0 +1,41 @@
+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
+
+inputs:
+  vcf:
+    type: File
+  clinvarvcf:
+    type: File
+outputs:
+  reporttxt: stdout
+
+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"
+  - {valueFrom: '|', shellQuote: false}
+  - bcftools
+  - query
+  - prefix: "-f"
+    valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"