3 label: WGS processing workflow scattered over samples
6 - class: SubworkflowFeatureRequirement
7 - class: ScatterFeatureRequirement
12 label: Directory of paired FASTQ files
15 format: edam:format_1929 # FASTA
16 label: Reference genome
30 format: edam:format_3016 # VCF
31 label: VCF of known polymorphic sites for BQSR
36 label: Desired split for variant calling
39 format: edam:format_3016 # VCF
40 label: Reference VCF for ClinVar
43 label: Function used to create HTML report
46 format: edam:format_1964 # HTML
47 label: Header for HTML report
50 format: edam:format_1964 # HTML
51 label: Footer for HTML report
56 outputSource: bwamem-gatk-report/gvcf
57 format: edam:format_3016 # GVCF
58 label: GVCFs generated from sets of fastqs
62 outputSource: bwamem-gatk-report/report
63 format: edam:format_1964 # HTML
64 label: ClinVar variant reports
68 run: ./helper/getfastq.cwl
71 out: [fastq1, fastq2, sample]
74 run: ./helper/bwamem-gatk-report-wf.cwl
75 scatter: [fastq1, fastq2, sample]
76 scatterMethod: dotproduct
78 fastq1: getfastq/fastq1
79 fastq2: getfastq/fastq2
81 sample: getfastq/sample
82 knownsites: knownsites
83 scattercount: scattercount
84 clinvarvcf: clinvarvcf
85 reportfunc: reportfunc
88 out: [qc-html,qc-zip,gvcf,report]
90 s:codeRepository: https://github.com/arvados/arvados-tutorial
91 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
94 s: https://schema.org/
95 edam: http://edamontology.org/
98 - https://schema.org/version/latest/schema.rdf
99 - http://edamontology.org/EDAM_1.18.owl