3 label: Scattered variant calling workflow
6 SubworkflowFeatureRequirement: {}
7 ScatterFeatureRequirement: {}
12 format: edam:format_2572 # BAM
13 label: Indexed sorted BAM with labeled duplicates
18 format: edam:format_1929 # FASTA
19 label: Reference genome
30 label: Full list of intervals to operate over
36 format: edam:format_3016 # VCF
37 label: VCF of known SNPS sites for BQSR
42 format: edam:format_3016 # VCF
43 label: VCF of known indel sites for BQSR
48 label: Desired split for variant calling
53 format: edam:format_3016 # GVCF
57 outputSource: gather-GVCFs/gatheredgvcf
61 run: gatk-splitintervals.cwl
64 fullintervallist: fullintervallist
66 scattercount: scattercount
69 recal-haplotypecaller:
70 run: gatk-wf-with-interval.cwl
76 knownsites1: knownsites1
77 knownsites2: knownsites2
78 intervallist: splitintervals/intervalfiles
82 run: gather-array-vcf.cwl
84 gvcfarray: recal-haplotypecaller/gvcf
89 s:codeRepository: https://github.com/arvados/arvados-tutorial
90 s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
93 s: https://schema.org/
94 edam: http://edamontology.org/
97 # - https://schema.org/version/latest/schema.rdf
98 # - http://edamontology.org/EDAM_1.18.owl