3 label: WGS processing workflow for single sample
6 - class: SubworkflowFeatureRequirement
11 format: edam:format_1930 # FASTQ
12 label: One of set of pair-end FASTQs (R1)
15 format: edam:format_1930 # FASTQ
16 label: One of set of pair-end FASTQs (R2)
19 format: edam:format_1929 # FASTA
20 label: Reference genome
34 format: edam:format_3016 # VCF
35 label: VCF of known polymorphic sites for BQSR
40 label: Desired split for variant calling
43 format: edam:format_3016 # VCF
44 label: Reference VCF for ClinVar
47 label: Function used to create HTML report
50 format: edam:format_1964 # HTML
51 label: Header for HTML report
54 format: edam:format_1964 # HTML
55 label: Footer for HTML report
60 label: FASTQ QC reports
61 format: edam:format_1964 # HTML
62 outputSource: fastqc/out-html
65 label: Zip files of FASTQ QC report and associated data
66 outputSource: fastqc/out-zip
69 outputSource: haplotypecaller/gatheredgvcf
70 format: edam:format_3016 # GVCF
71 label: GVCF generated from GATK Haplotype Caller
74 outputSource: generate-report/report
75 format: edam:format_1964 # HTML
76 label: ClinVar variant report
84 out: [out-html, out-zip]
86 run: bwamem-samtools-view.cwl
94 run: samtools-sort.cwl
96 bam: bwamem-samtools-view/bam
100 run: mark-duplicates.cwl
102 bam: samtools-sort/sortedbam
103 out: [dupbam,dupmetrics]
105 run: samtools-index.cwl
107 bam: mark-duplicates/dupbam
110 run: scatter-gatk-wf-with-interval.cwl
113 bam: samtools-index/indexedbam
115 scattercount: scattercount
116 knownsites: knownsites
121 gvcf: haplotypecaller/gatheredgvcf
123 clinvarvcf: clinvarvcf
124 reportfunc: reportfunc
129 s:codeRepository: https://github.com/arvados/arvados-tutorial
130 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
133 s: https://schema.org/
134 edam: http://edamontology.org/
137 - https://schema.org/version/latest/schema.rdf
138 - http://edamontology.org/EDAM_1.18.owl