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Adding metatdata and labels
[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
index 310753c5c458b849d767e027cae696f8e462576a..41ec58cd35fab6638dd47f2bf078e8d3a032c55a 100644
(file)
--- a/
WGS-processing/cwl/helper/annotate-vcf.cwl
+++ b/
WGS-processing/cwl/helper/annotate-vcf.cwl
@@
-11,14
+11,24
@@
hints:
ResourceRequirement:
ramMin: 10000
coresMin: 4
ResourceRequirement:
ramMin: 10000
coresMin: 4
+ SoftwareRequirement:
+ packages:
+ BCFtools:
+ specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
+ version: [ "1.10.2" ]
stdout: $(inputs.vcf.nameroot).txt
inputs:
vcf:
type: File
stdout: $(inputs.vcf.nameroot).txt
inputs:
vcf:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF extracted from GVCF
+ secondaryFiles: [.tbi]
clinvarvcf:
type: File
clinvarvcf:
type: File
+ format: edam:format_3016 # VCF
+ label: Reference VCF for ClinVar
outputs:
reporttxt: stdout
outputs:
reporttxt: stdout
@@
-41,3
+51,11
@@
arguments:
- query
- prefix: "-f"
valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"
- query
- prefix: "-f"
valueFrom: "%ID\t%CHROM\t%POS\t%REF\t%ALT\t%INFO/ALLELEID\t%INFO/CLNSIG\t%INFO/CLNDN\t%INFO/AF_ESP\t%INFO/AF_EXAC\t%INFO/AF_TGP[\t%GT]\n"
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl