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annotator_sub_wf.cwl
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annotator_sub_wf.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
doc: |
This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be
run as a stand-alone workflow!
requirements:
- class: SchemaDefRequirement
types:
- $import: TumourType.yaml
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
expressionLib:
- { $include: oxog_varbam_annotate_util.js }
- class: SubworkflowFeatureRequirement
inputs:
tumour_record:
type: "TumourType.yaml#TumourType"
tumourMinibams:
type: File[]
VCFs:
type: File[]
normalMinibam:
type: File
variantType:
type: string
outputs:
annotated_vcfs:
type: File[]
outputSource: level_0/annotated_vcf
steps:
# This step will prepare the next level by creating vcfsToAnnotate as an array of
# vcfs that need to be annotated
level_0:
in:
vcfsToAnnotate:
source: [tumour_record, VCFs]
valueFrom: |
${
return chooseVCFsForAnnotator(self[1], self[0].associatedVcfs)
}
tumour_bam:
source: [tumour_record, tumourMinibams]
valueFrom: |
${
return chooseMiniBamForAnnotator(self[1], self[0])
}
variantType: variantType
normalMinibam: normalMinibam
out: [annotated_vcf]
run:
class: Workflow
inputs:
tumour_bam:
type: File
vcfsToAnnotate:
type: File[]
variantType:
type: string
normalMinibam:
type: File
outputs:
annotated_vcf:
type: File[]
outputSource: level_1/annotated_vcf
steps:
# This step scatters across the array of VCFs created by level_0
level_1:
in:
tumour_bam: tumour_bam
input_vcf: vcfsToAnnotate
variant_type: variantType
normal_bam: normalMinibam
scatter: [input_vcf]
out:
[annotated_vcf]
run:
class: Workflow
inputs:
tumour_bam:
type: File
input_vcf:
type: File
variant_type:
type: string
normal_bam:
type: File
steps:
# This step takes the scatter of level_1 and executes the annotator on each VCF.
level_2:
in:
tumour_bam: tumour_bam
input_vcf: input_vcf
variant_type: variant_type
normal_bam: normal_bam
output:
source: [input_vcf]
valueFrom: |
${
return self.basename.replace('.vcf.gz','_annotated.vcf')
}
out:
[annotated_vcf]
run:
sga-annotate-docker/Dockstore.cwl
outputs:
annotated_vcf:
type: File
outputSource: level_2/annotated_vcf