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filtering.cwl
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filtering.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
SchemaDefRequirement:
types:
- $import: ../../resources/schemas/params/basic-filtering-vardict.yaml
- $import: ../../resources/schemas/params/basic-filtering-mutect.yaml
inputs:
basicfiltering_vardict_params: ../../resources/schemas/params/basic-filtering-vardict.yaml#basicfiltering_vardict_params
basicfiltering_mutect_params: ../../resources/schemas/params/basic-filtering-mutect.yaml#basicfiltering_mutect_params
mutect_vcf: File
mutect_callstats: File
vardict_vcf: File
tumor_sample_name: string
normal_sample_name: string
ref_fasta: File
outputs:
vardict_norm_vcf:
type: File
outputSource: vardict_filtering_step/vcf
secondaryFiles: [.tbi]
mutect_norm_vcf:
type: File
outputSource: mutect_filtering_step/vcf
secondaryFiles: [.tbi]
steps:
mutect_filtering_step:
run: ../../cwl_tools/basicfiltering/basic-filtering_mutect.cwl
in:
basicfiltering_mutect_params: basicfiltering_mutect_params
total_depth:
valueFrom: $(inputs.basicfiltering_mutect_params.total_depth)
allele_depth:
valueFrom: $(inputs.basicfiltering_mutect_params.allele_depth)
tumor_normal_ratio:
valueFrom: $(inputs.basicfiltering_mutect_params.tumor_normal_ratio)
variant_fraction:
valueFrom: $(inputs.basicfiltering_mutect_params.variant_fraction)
inputVcf: mutect_vcf
inputTxt: mutect_callstats
tsampleName: tumor_sample_name
refFasta: ref_fasta
out: [vcf]
vardict_filtering_step:
run: ../../cwl_tools/basicfiltering/basic-filtering_vardict.cwl
in:
basicfiltering_vardict_params: basicfiltering_vardict_params
total_depth:
valueFrom: $(inputs.basicfiltering_vardict_params.total_depth)
allele_depth:
valueFrom: $(inputs.basicfiltering_vardict_params.allele_depth)
tumor_normal_ratio:
valueFrom: $(inputs.basicfiltering_vardict_params.tumor_normal_ratio)
variant_fraction:
valueFrom: $(inputs.basicfiltering_vardict_params.variant_fraction)
filter_germline:
valueFrom: $(inputs.basicfiltering_vardict_params.filter_germline)
min_qual:
valueFrom: $(inputs.basicfiltering_vardict_params.min_qual)
inputVcf: vardict_vcf
tsampleName: tumor_sample_name
refFasta: ref_fasta
out: [vcf]