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filter_vcf.cwl
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filter_vcf.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Apply filters to VCF file"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
vcf:
type: File
filter_mapq0_threshold:
type: float
filter_gnomADe_maximum_population_allele_frequency:
type: float
tumor_bam:
type: File
secondaryFiles: [.bai]
do_cle_vcf_filter:
type: boolean
filter_somatic_llr_threshold:
type: float
reference:
type: string
outputs:
filtered_vcf:
type: File
outputSource: filter_vcf_cle/cle_filtered_vcf
secondaryFiles: [.tbi]
steps:
filter_vcf_gnomADe_allele_freq:
run: ../tools/filter_vcf_gnomADe_allele_freq.cwl
in:
vcf: vcf
maximum_population_allele_frequency: filter_gnomADe_maximum_population_allele_frequency
out:
[filtered_vcf]
filter_vcf_mapq0:
run: ../tools/filter_vcf_mapq0.cwl
in:
vcf: filter_vcf_gnomADe_allele_freq/filtered_vcf
tumor_bam: tumor_bam
threshold: filter_mapq0_threshold
reference: reference
out:
[mapq0_filtered_vcf]
filter_vcf_cle:
run: ../tools/filter_vcf_cle.cwl
in:
vcf: filter_vcf_mapq0/mapq0_filtered_vcf
filter: do_cle_vcf_filter
out:
[cle_filtered_vcf]
filter_vcf_somatic_llr:
run: ../tools/filter_vcf_somatic_llr.cwl
in:
vcf: filter_vcf_cle/cle_filtered_vcf
threshold: filter_somatic_llr_threshold
out:
[somatic_llr_filtered_vcf]