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tumor_only_detect_variants.cwl
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tumor_only_detect_variants.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Tumor-Only Detect Variants workflow"
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: SchemaDefRequirement
types:
- $import: ../types/vep_custom_annotation.yml
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .index]
bam:
type: File
secondaryFiles: [^.bai,.bai]
interval_list:
type: File
varscan_strand_filter:
type: int?
default: 0
varscan_min_coverage:
type: int?
default: 8
varscan_min_var_freq:
type: float?
default: 0.1
varscan_p_value:
type: float?
default: 0.99
varscan_min_reads:
type: int?
default: 2
maximum_population_allele_frequency:
type: float?
default: 0.001
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"
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
default: true
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
variants_to_table_fields:
type: string[]?
default: [CHROM,POS,REF,ALT,set]
variants_to_table_genotype_fields:
type: string[]?
default: [GT,AD,AF,DP]
vep_to_table_fields:
type: string[]?
default: [Consequence,SYMBOL,Feature_type,Feature,HGVSc,HGVSp,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,HGNC_ID,Existing_variation,gnomADe_AF,CLIN_SIG,SOMATIC,PHENO]
vep_plugins:
type: string[]?
default: [Downstream, Wildtype]
sample_name:
type: string
docm_vcf:
type: File
secondaryFiles: [.tbi]
vep_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
readcount_minimum_mapping_quality:
type: int?
readcount_minimum_base_quality:
type: int?
outputs:
varscan_vcf:
type: File
outputSource: varscan/unfiltered_vcf
secondaryFiles: [.tbi]
docm_gatk_vcf:
type: File
outputSource: docm/unfiltered_vcf
annotated_vcf:
type: File
outputSource: index/indexed_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: index_filtered/indexed_vcf
secondaryFiles: [.tbi]
final_tsv:
type: File
outputSource: add_vep_fields_to_table/annotated_variants_tsv
vep_summary:
type: File
outputSource: annotate_variants/vep_summary
tumor_snv_bam_readcount_tsv:
type: File
outputSource: bam_readcount/snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv:
type: File
outputSource: bam_readcount/indel_bam_readcount_tsv
steps:
varscan:
run: ../subworkflows/varscan_germline.cwl
in:
reference: reference
bam: bam
interval_list: interval_list
strand_filter: varscan_strand_filter
min_coverage: varscan_min_coverage
min_var_freq: varscan_min_var_freq
min_reads: varscan_min_reads
p_value: varscan_p_value
sample_name: sample_name
out:
[unfiltered_vcf, filtered_vcf]
docm:
run: ../subworkflows/docm_germline.cwl
in:
reference: reference
bam: bam
interval_list: interval_list
docm_vcf: docm_vcf
out:
[unfiltered_vcf, filtered_vcf]
combine_variants:
run: ../tools/germline_combine_variants.cwl
in:
reference: reference
varscan_vcf: varscan/filtered_vcf
docm_vcf: docm/filtered_vcf
out:
[combined_vcf]
decompose:
run: ../tools/vt_decompose.cwl
in:
vcf: combine_variants/combined_vcf
out:
[decomposed_vcf]
annotate_variants:
run: ../tools/vep.cwl
in:
vcf: decompose/decomposed_vcf
cache_dir: vep_cache_dir
synonyms_file: synonyms_file
coding_only: annotate_coding_only
reference: reference
custom_annotations: vep_custom_annotations
pick: vep_pick
ensembl_assembly: vep_ensembl_assembly
ensembl_version: vep_ensembl_version
ensembl_species: vep_ensembl_species
plugins: vep_plugins
out:
[annotated_vcf, vep_summary]
bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: annotate_variants/annotated_vcf
sample: sample_name
reference_fasta: reference
bam: bam
min_mapping_quality: readcount_minimum_mapping_quality
min_base_quality: readcount_minimum_base_quality
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]
add_bam_readcount_to_vcf:
run: ../subworkflows/vcf_readcount_annotator.cwl
in:
vcf: annotate_variants/annotated_vcf
snv_bam_readcount_tsv: bam_readcount/snv_bam_readcount_tsv
indel_bam_readcount_tsv: bam_readcount/indel_bam_readcount_tsv
data_type:
default: 'DNA'
sample_name: sample_name
out:
[annotated_bam_readcount_vcf]
index:
run: ../tools/index_vcf.cwl
in:
vcf: add_bam_readcount_to_vcf/annotated_bam_readcount_vcf
out:
[indexed_vcf]
hard_filter:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: index/indexed_vcf
interval_list: interval_list
exclude_filtered:
default: true
out:
[filtered_vcf]
af_filter:
run: ../tools/filter_vcf_custom_allele_freq.cwl
in:
vcf: hard_filter/filtered_vcf
maximum_population_allele_frequency: maximum_population_allele_frequency
field_name:
source: vep_custom_annotations
valueFrom: |
${
if(self){
for(var i=0; i<self.length; i++){
if(self[i].annotation.gnomad_filter){
return(self[i].annotation.name + '_AF');
}
}
}
return('gnomAD_AF');
}
out:
[filtered_vcf]
coding_variant_filter:
run: ../tools/filter_vcf_coding_variant.cwl
in:
vcf: af_filter/filtered_vcf
out:
[filtered_vcf]
bgzip_filtered:
run: ../tools/bgzip.cwl
in:
file: coding_variant_filter/filtered_vcf
out:
[bgzipped_file]
index_filtered:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip_filtered/bgzipped_file
out:
[indexed_vcf]
variants_to_table:
run: ../tools/variants_to_table.cwl
in:
reference: reference
vcf: index_filtered/indexed_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: index_filtered/indexed_vcf
vep_fields: vep_to_table_fields
tsv: variants_to_table/variants_tsv
out: [annotated_variants_tsv]