3 label: Annotate and filter VCF
6 - class: DockerRequirement
7 dockerPull: curii/clinvar-report
8 - class: ShellCommandRequirement
17 specs: [ "https://identifiers.org/rrid/RRID:SCR_005227" ]
20 stdout: $(inputs.vcf.nameroot).txt
25 format: edam:format_3016 # VCF
26 label: VCF extracted from GVCF
27 secondaryFiles: [.tbi]
30 format: edam:format_3016 # VCF
31 label: Reference VCF for ClinVar
40 valueFrom: $(inputs.clinvarvcf.path)
44 - {valueFrom: '|', shellQuote: false}
48 valueFrom: "INFO/ALLELEID>=1"
49 - {valueFrom: '|', shellQuote: false}
53 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"
56 s: https://schema.org/
57 edam: http://edamontology.org/
60 - https://schema.org/version/latest/schema.rdf
61 - http://edamontology.org/EDAM_1.18.owl