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
29 format: edam:format_3016 # VCF
30 label: VCF of known SNPS sites for BQSR
35 format: edam:format_3016 # VCF
36 label: VCF of known indel sites for BQSR
41 label: Desired split for variant calling
44 format: edam:format_3016 # VCF
45 label: Reference VCF for ClinVar
48 label: Function used to create HTML report
51 format: edam:format_2331 # HTML
52 label: Header for HTML report
55 format: edam:format_2331 # HTML
56 label: Footer for HTML report
61 outputSource: bwamem-gatk-report/gvcf
62 format: edam:format_3016 # GVCF
63 label: GVCFs generated from GATK
66 outputSource: bwamem-gatk-report/report
67 format: edam:format_2331 # HTML
68 label: ClinVar variant reports
72 run: ./helper/getfastq.cwl
75 out: [fastq1, fastq2, sample]
78 run: ./helper/bwamem-gatk-report-wf.cwl
79 scatter: [fastq1, fastq2, sample]
80 scatterMethod: dotproduct
82 fastq1: getfastq/fastq1
83 fastq2: getfastq/fastq2
85 fullintervallist: fullintervallist
86 sample: getfastq/sample
87 knownsites1: knownsites1
88 knownsites2: knownsites2
89 scattercount: scattercount
90 clinvarvcf: clinvarvcf
91 reportfunc: reportfunc
94 out: [qc-html,qc-zip,gvcf,report]
96 s:codeRepository: https://github.com/arvados/arvados-tutorial
97 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
100 s: https://schema.org/
101 edam: http://edamontology.org/
104 # - https://schema.org/version/latest/schema.rdf
105 # - http://edamontology.org/EDAM_1.18.owl