-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
cwlVersion: v1.1
class: Workflow
+label: Variant calling workflow scattered over interval splits
requirements:
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Indexed sorted BAM with labeled duplicates
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- .sa
- .fai
- ^.dict
- sample: string
+ sample:
+ type: string
+ label: Sample Name
knownsites1:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
- scattercount: string
+ scattercount:
+ type: string
+ label: Desired split for variant calling
outputs:
gatheredgvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: GVCF generated from GATK Haplotype Caller
secondaryFiles:
- .tbi
outputSource: merge-GVCFs/gatheredgvcf
sample: sample
reference: reference
out: [gatheredgvcf]
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl