3 label: Filter unused alternates
7 dockerPull: broadinstitute/gatk:4.1.7.0
10 arv:RuntimeConstraints:
11 outputDirType: keep_output_dir
19 specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
25 format: edam:format_3016 # GVCF
26 label: GVCF for given interval
31 format: edam:format_1929 # FASTA
32 label: Reference genome
48 format: edam:format_3016 # GVCF
49 label: Given interval filtered GVCF
53 baseCommand: /gatk/gatk
60 valueFrom: $(inputs.reference)
61 - prefix: "--remove-unused-alternates"
64 valueFrom: $(inputs.gvcf.path)
66 valueFrom: selected$(inputs.gvcf.basename)
68 s:codeRepository: https://github.com/arvados/arvados-tutorial
69 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
72 s: https://schema.org/
73 edam: http://edamontology.org/
74 arv: "http://arvados.org/cwl#"
75 cwltool: "http://commonwl.org/cwltool#"
78 # - https://schema.org/version/latest/schema.rdf
79 # - http://edamontology.org/EDAM_1.18.owl