Rearranging for clarity

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

diff --git a/cwl/helper/annotate-vcf.cwl b/cwl/helper/annotate-vcf.cwl
deleted file mode 100644 (file)
index 019fa1a..0000000
--- a/cwl/helper/annotate-vcf.cwl
+++ /dev/null
@@ -1,41 +0,0 @@
-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"