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
27 format: edam:format_3016 # VCF
28 label: VCF of known polymorphic sites for BQSR
33 label: Desired split for variant calling
36 format: edam:format_3016 # VCF
37 label: Reference VCF for ClinVar
40 label: Function used to create HTML report
43 format: edam:format_2331 # HTML
44 label: Header for HTML report
47 format: edam:format_2331 # HTML
48 label: Footer for HTML report
53 outputSource: bwamem-gatk-report/gvcf
54 format: edam:format_3016 # GVCF
55 label: GVCFs generated from GATK
58 outputSource: bwamem-gatk-report/report
59 format: edam:format_2331 # HTML
60 label: ClinVar variant reports
64 run: ./helper/getfastq.cwl
67 out: [fastq1, fastq2, sample]
70 run: ./helper/bwamem-gatk-report-wf.cwl
71 scatter: [fastq1, fastq2, sample]
72 scatterMethod: dotproduct
74 fastq1: getfastq/fastq1
75 fastq2: getfastq/fastq2
77 sample: getfastq/sample
78 knownsites: knownsites
79 scattercount: scattercount
80 clinvarvcf: clinvarvcf
81 reportfunc: reportfunc
84 out: [qc-html,qc-zip,gvcf,report]
86 s:codeRepository: https://github.com/arvados/arvados-tutorial
87 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
90 s: https://schema.org/
91 edam: http://edamontology.org/
94 # - https://schema.org/version/latest/schema.rdf
95 # - http://edamontology.org/EDAM_1.18.owl