/
germline_detect_variants.cwl
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germline_detect_variants.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment and germline variant detection"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference:
type: string
bam:
type: File
emit_reference_confidence:
type: string
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
contamination_fraction:
type: string?
vep_cache_dir:
type: string
vep_ensembl_assembly:
type: string
doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38"
vep_ensembl_version:
type: string
doc: "ensembl version - Must be present in the cache directory. Example: 95"
vep_ensembl_species:
type: string
doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus"
vep_plugins:
type: string[]?
default: [Downstream, Wildtype]
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
limit_variant_intervals:
type: File
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
variants_to_table_fields:
type: string[]?
default: ['CHROM','POS','ID','REF','ALT']
variants_to_table_genotype_fields:
type: string[]?
vep_to_table_fields:
type: string[]?
final_tsv_prefix:
type: string?
default: 'variants'
outputs:
gvcf:
type: File[]
outputSource: haplotype_caller/gvcf
final_vcf:
type: File
outputSource: index_annotated_vcf/indexed_vcf
secondaryFiles: [.tbi]
coding_vcf:
type: File
outputSource: index_coding_vcf/indexed_vcf
secondaryFiles: [.tbi]
limited_vcf:
type: File
outputSource: limit_variants/filtered_vcf
secondaryFiles: [.tbi]
vep_summary:
type: File
outputSource: annotate_variants/vep_summary
final_tsv:
type: File
outputSource: add_vep_fields_to_table/annotated_variants_tsv
steps:
haplotype_caller:
run: gatk_haplotypecaller_iterator.cwl
in:
reference: reference
bam: bam
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
contamination_fraction: contamination_fraction
out:
[gvcf]
genotype_gvcfs:
run: ../tools/gatk_genotypegvcfs.cwl
in:
reference: reference
gvcfs: haplotype_caller/gvcf
out:
[genotype_vcf]
annotate_variants:
run: ../tools/vep.cwl
in:
vcf: genotype_gvcfs/genotype_vcf
cache_dir: vep_cache_dir
ensembl_assembly: vep_ensembl_assembly
ensembl_version: vep_ensembl_version
ensembl_species: vep_ensembl_species
synonyms_file: synonyms_file
coding_only: annotate_coding_only
reference: reference
custom_gnomad_vcf: custom_gnomad_vcf
custom_clinvar_vcf: custom_clinvar_vcf
plugins: vep_plugins
out:
[annotated_vcf, vep_summary]
bgzip_annotated_vcf:
run: ../tools/bgzip.cwl
in:
file: annotate_variants/annotated_vcf
out:
[bgzipped_file]
index_annotated_vcf:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip_annotated_vcf/bgzipped_file
out:
[indexed_vcf]
coding_variant_filter:
run: ../tools/filter_vcf_coding_variant.cwl
in:
vcf: annotate_variants/annotated_vcf
out:
[filtered_vcf]
bgzip_coding_vcf:
run: ../tools/bgzip.cwl
in:
file: coding_variant_filter/filtered_vcf
out:
[bgzipped_file]
index_coding_vcf:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip_coding_vcf/bgzipped_file
out:
[indexed_vcf]
limit_variants:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: index_coding_vcf/indexed_vcf
interval_list: limit_variant_intervals
exclude_filtered:
default: true
out:
[filtered_vcf]
variants_to_table:
run: ../tools/variants_to_table.cwl
in:
reference: reference
vcf: limit_variants/filtered_vcf
fields: variants_to_table_fields
genotype_fields: variants_to_table_genotype_fields
out:
[variants_tsv]
add_vep_fields_to_table:
run: ../tools/add_vep_fields_to_table.cwl
in:
vcf: limit_variants/filtered_vcf
vep_fields: vep_to_table_fields
tsv: variants_to_table/variants_tsv
prefix: final_tsv_prefix
out: [annotated_variants_tsv]