cwlVersion: v1.1
class: Workflow
+label: Variant calling workflow for single interval
requirements:
- class: SubworkflowFeatureRequirement
steps:
basecalibrator:
- run: ./helper/gatk-baserecalibrator-with-interval.cwl
+ run: gatk-baserecalibrator-with-interval.cwl
in:
bam: bam
reference: reference
intervallist: intervallist
out: [recaltable]
applyBQSR:
- run: ./helper/gatk-applyBSQR-with-interval.cwl
+ run: gatk-applyBSQR-with-interval.cwl
in:
reference: reference
bam: bam
recaltable: basecalibrator/recaltable
out: [recalbam]
haplotypecaller:
- run: ./helper/gatk-haplotypecaller-with-interval.cwl
+ run: gatk-haplotypecaller-with-interval.cwl
in:
reference: reference
bam: applyBQSR/recalbam
intervallist: intervallist
out: [gvcf]
selectvariants:
- run: ./helper/gatk-selectvariants.cwl
+ run: gatk-selectvariants.cwl
in:
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
out: [filteredgvcf]
+
+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