-$namespaces:
- arv: "http://arvados.org/cwl#"
- cwltool: "http://commonwl.org/cwltool#"
cwlVersion: v1.1
class: Workflow
+label: Scattered variant calling workflow
requirements:
- - class: SubworkflowFeatureRequirement
- - class: ScatterFeatureRequirement
+ SubworkflowFeatureRequirement: {}
+ ScatterFeatureRequirement: {}
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
+ fullintervallist:
+ type: File
+ label: Full list of intervals to operate over
+ sample:
+ type: string
+ label: Sample Name
knownsites1:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known SNPS sites for BQSR
+ secondaryFiles:
+ - .idx
+ knownsites2:
+ type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known indel sites for BQSR
secondaryFiles:
- .tbi
- scattercount: string
+ scattercount:
+ type: string
+ label: Desired split for variant calling
outputs:
gatheredgvcf:
type: File
- secondaryFiles:
+ format: edam:format_3016 # GVCF
+ label: Gathered GVCF
+ secondaryFiles:
- .tbi
- outputSource: merge-GVCFs/gatheredgvcf
+ outputSource: gather-GVCFs/gatheredgvcf
steps:
splitintervals:
run: gatk-splitintervals.cwl
in:
reference: reference
+ fullintervallist: fullintervallist
sample: sample
scattercount: scattercount
out: [intervalfiles]
- recal-haplotypecaller:
+ recal-haplotypecaller:
run: gatk-wf-with-interval.cwl
scatter: intervallist
in:
reference: reference
sample: sample
knownsites1: knownsites1
+ knownsites2: knownsites2
intervallist: splitintervals/intervalfiles
out: [gvcf]
- merge-GVCFs:
+ gather-GVCFs:
run: gather-array-vcf.cwl
in:
gvcfarray: recal-haplotypecaller/gvcf
sample: sample
reference: reference
- out: [gatheredgvcf]
+ 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