3 label: Generate recalibration table for BQSR
7 dockerPull: broadinstitute/gatk:4.1.7.0
8 InitialWorkDirRequirement:
13 arv:RuntimeConstraints:
14 outputDirType: keep_output_dir
22 specs: [ "https://identifiers.org/rrid/RRID:SCR_001876" ]
28 format: edam:format_2572 # BAM
29 label: Indexed sorted BAM with labeled duplicates
34 format: edam:format_1929 # FASTA
35 label: Reference genome
49 format: edam:format_3016 # VCF
50 label: VCF of known polymorphic sites for BQSR
55 label: Scatter intervals file
60 label: Recalibration table for given interval
64 baseCommand: /gatk/gatk
71 valueFrom: $(inputs.reference)
73 valueFrom: $(inputs.bam.basename)
74 - prefix: "--known-sites"
75 valueFrom: $(inputs.knownsites)
77 valueFrom: $(inputs.intervallist)
79 valueFrom: $(inputs.sample)_recal_data.table
81 s:codeRepository: https://github.com/arvados/arvados-tutorial
82 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
85 s: https://schema.org/
86 edam: http://edamontology.org/
87 arv: "http://arvados.org/cwl#"
88 cwltool: "http://commonwl.org/cwltool#"
91 - https://schema.org/version/latest/schema.rdf
92 - http://edamontology.org/EDAM_1.18.owl