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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
- class: StepInputExpressionRequirement
- class: MultipleInputFeatureRequirement
inputs:
vcf:
type: File
secondaryFiles: [.tbi]
filter_mapq0_threshold:
type: float
filter_gnomADe_maximum_population_allele_frequency:
type: float
gnomad_field_name:
type: string
tumor_bam:
type: File
secondaryFiles: [.bai]
do_cle_vcf_filter:
type: boolean
filter_somatic_llr_threshold:
type: float
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
filter_minimum_depth:
type: int
tumor_sample_name:
type: string
normal_sample_name:
type: string
known_variants:
type: File?
secondaryFiles: [.tbi]
doc: "Previously discovered variants to be flagged in this workflow's output vcf"
outputs:
filtered_vcf:
type: File
outputSource: set_final_vcf_name/replacement
steps:
filter_known_variants:
run: ../tools/filter_known_variants.cwl
in:
known_variants: known_variants
vcf: vcf
out:
[known_filtered]
filter_vcf_gnomADe_allele_freq:
run: ../tools/filter_vcf_custom_allele_freq.cwl
in:
vcf: filter_known_variants/known_filtered
maximum_population_allele_frequency: filter_gnomADe_maximum_population_allele_frequency
field_name: gnomad_field_name
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_depth:
run: ../tools/filter_vcf_depth.cwl
in:
vcf: filter_vcf_cle/cle_filtered_vcf
minimum_depth: filter_minimum_depth
sample_names:
source: [normal_sample_name, tumor_sample_name]
linkMerge: merge_flattened
out:
[depth_filtered_vcf]
filter_vcf_somatic_llr:
run: ../tools/filter_vcf_somatic_llr.cwl
in:
vcf: filter_vcf_depth/depth_filtered_vcf
threshold: filter_somatic_llr_threshold
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[somatic_llr_filtered_vcf]
set_final_vcf_name:
run: ../tools/staged_rename.cwl
in:
original: filter_vcf_somatic_llr/somatic_llr_filtered_vcf
name:
valueFrom: 'annotated_filtered.vcf'
out:
[replacement]