3 label: Marking Duplicates using GATK (Picard)
7 dockerPull: broadinstitute/gatk:4.1.7.0
13 arv:RuntimeConstraints:
14 outputDirType: keep_output_dir
18 specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
24 format: edam:format_2572 # BAM
30 format: edam:format_2572 # BAM
31 label: Sorted BAM with labeled duplicates
36 label: Duplication metrics file
40 baseCommand: /gatk/gatk
47 valueFrom: $(inputs.bam.path)
49 valueFrom: marked_dups$(inputs.bam.basename)
51 valueFrom: "metrics.txt"
53 s:codeRepository: https://github.com/arvados/arvados-tutorial
54 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
57 s: https://schema.org/
58 edam: http://edamontology.org/
59 arv: "http://arvados.org/cwl#"
60 cwltool: "http://commonwl.org/cwltool#"
63 - https://schema.org/version/latest/schema.rdf
64 - http://edamontology.org/EDAM_1.18.owl