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detect_variants.cwl
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detect_variants.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Detect Variants workflow"
requirements:
- class: SubworkflowFeatureRequirement
inputs:
reference:
type: string
tumor_bam:
type: File
secondaryFiles: [.bai,^.bai]
normal_bam:
type: File
secondaryFiles: [.bai,^.bai]
interval_list:
type: File
dbsnp_vcf:
type: File?
secondaryFiles: [.tbi]
cosmic_vcf:
type: File?
secondaryFiles: [.tbi]
panel_of_normals_vcf:
type: File?
secondaryFiles: [.tbi]
strelka_exome_mode:
type: boolean
strelka_cpu_reserved:
type: int?
default: 8
readcount_minimum_base_quality:
type: int?
readcount_minimum_mapping_quality:
type: int?
mutect_scatter_count:
type: int?
mutect_artifact_detection_mode:
type: boolean?
mutect_max_alt_allele_in_normal_fraction:
type: float?
mutect_max_alt_alleles_in_normal_count:
type: int?
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_max_normal_freq:
type: float?
pindel_insert_size:
type: int
default: 400
docm_vcf:
type: File
secondaryFiles: [.tbi]
filter_docm_variants:
type: boolean?
default: true
vep_cache_dir:
type: string
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
filter_gnomADe_maximum_population_allele_frequency:
type: float?
default: 0.001
filter_mapq0_threshold:
type: float?
default: 0.15
filter_minimum_depth:
type: int?
default: 1
cle_vcf_filter:
type: boolean?
default: false
filter_somatic_llr_threshold:
type: float?
default: 5
variants_to_table_fields:
type: string[]?
default: [CHROM,POS,ID,REF,ALT,set,AC,AF,FILTER]
variants_to_table_genotype_fields:
type: string[]?
default: [GT,AD]
vep_to_table_fields:
type: string[]?
default: [HGVSc,HGVSp,Consequence,SYMBOL,Gene,Feature_type,Feature,Existing_variation,SYMBOL_SOURCE]
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
outputs:
mutect_unfiltered_vcf:
type: File
outputSource: mutect/unfiltered_vcf
secondaryFiles: [.tbi]
strelka_unfiltered_vcf:
type: File
outputSource: strelka/unfiltered_vcf
secondaryFiles: [.tbi]
varscan_unfiltered_vcf:
type: File
outputSource: varscan/unfiltered_vcf
secondaryFiles: [.tbi]
pindel_unfiltered_vcf:
type: File
outputSource: pindel/unfiltered_vcf
secondaryFiles: [.tbi]
docm_filtered_vcf:
type: File
outputSource: docm/docm_variants_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: index/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: tumor_bam_readcount/snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv:
type: File
outputSource: tumor_bam_readcount/indel_bam_readcount_tsv
normal_snv_bam_readcount_tsv:
type: File
outputSource: normal_bam_readcount/snv_bam_readcount_tsv
normal_indel_bam_readcount_tsv:
type: File
outputSource: normal_bam_readcount/indel_bam_readcount_tsv
steps:
mutect:
run: ../subworkflows/mutect.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
interval_list: interval_list
dbsnp_vcf: dbsnp_vcf
cosmic_vcf: cosmic_vcf
max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction
max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_count
scatter_count: mutect_scatter_count
artifact_detection_mode: mutect_artifact_detection_mode
panel_of_normals_vcf: panel_of_normals_vcf
out:
[unfiltered_vcf]
strelka:
run: ../subworkflows/strelka_and_post_processing.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
interval_list: interval_list
exome_mode: strelka_exome_mode
cpu_reserved: strelka_cpu_reserved
out:
[unfiltered_vcf]
varscan:
run: ../subworkflows/varscan_pre_and_post_processing.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
interval_list: interval_list
strand_filter: varscan_strand_filter
min_coverage: varscan_min_coverage
min_var_freq: varscan_min_var_freq
p_value: varscan_p_value
max_normal_freq: varscan_max_normal_freq
out:
[unfiltered_vcf]
pindel:
run: ../subworkflows/pindel.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
interval_list: interval_list
insert_size: pindel_insert_size
out:
[unfiltered_vcf]
docm:
run: ../subworkflows/docm_cle.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
docm_vcf: docm_vcf
interval_list: interval_list
filter_docm_variants: filter_docm_variants
out:
[docm_variants_vcf]
combine:
run: ../tools/combine_variants.cwl
in:
reference: reference
mutect_vcf: mutect/unfiltered_vcf
strelka_vcf: strelka/unfiltered_vcf
varscan_vcf: varscan/unfiltered_vcf
pindel_vcf: pindel/unfiltered_vcf
out:
[combined_vcf]
decompose:
run: ../tools/vt_decompose.cwl
in:
vcf: combine/combined_vcf
out:
[decomposed_vcf]
decompose_index:
run: ../tools/index_vcf.cwl
in:
vcf: decompose/decomposed_vcf
out:
[indexed_vcf]
add_docm_variants:
run: ../tools/docm_add_variants.cwl
in:
reference: reference
docm_vcf: docm/docm_variants_vcf
callers_vcf: decompose_index/indexed_vcf
out:
[merged_vcf]
annotate_variants:
run: ../tools/vep.cwl
in:
vcf: add_docm_variants/merged_vcf
cache_dir: vep_cache_dir
synonyms_file: synonyms_file
coding_only: annotate_coding_only
reference: reference
custom_gnomad_vcf: custom_gnomad_vcf
pick: vep_pick
custom_clivnar_vcf: custom_clinvar_vcf
out:
[annotated_vcf, vep_summary]
tumor_bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: annotate_variants/annotated_vcf
sample:
default: 'TUMOR'
reference_fasta: reference
bam: tumor_bam
min_base_quality: readcount_minimum_base_quality
min_mapping_quality: readcount_minimum_mapping_quality
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]
normal_bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: annotate_variants/annotated_vcf
sample:
default: 'NORMAL'
reference_fasta: reference
bam: normal_bam
min_base_quality: readcount_minimum_base_quality
min_mapping_quality: readcount_minimum_mapping_quality
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv]
add_tumor_bam_readcount_to_vcf:
run: ../subworkflows/vcf_readcount_annotator.cwl
in:
vcf: annotate_variants/annotated_vcf
snv_bam_readcount_tsv: tumor_bam_readcount/snv_bam_readcount_tsv
indel_bam_readcount_tsv: tumor_bam_readcount/indel_bam_readcount_tsv
data_type:
default: 'DNA'
sample_name:
default: 'TUMOR'
out:
[annotated_bam_readcount_vcf]
add_normal_bam_readcount_to_vcf:
run: ../subworkflows/vcf_readcount_annotator.cwl
in:
vcf: add_tumor_bam_readcount_to_vcf/annotated_bam_readcount_vcf
snv_bam_readcount_tsv: normal_bam_readcount/snv_bam_readcount_tsv
indel_bam_readcount_tsv: normal_bam_readcount/indel_bam_readcount_tsv
data_type:
default: 'DNA'
sample_name:
default: 'NORMAL'
out:
[annotated_bam_readcount_vcf]
index:
run: ../tools/index_vcf.cwl
in:
vcf: add_normal_bam_readcount_to_vcf/annotated_bam_readcount_vcf
out:
[indexed_vcf]
variants_to_table:
run: ../tools/variants_to_table.cwl
in:
reference: reference
vcf: index/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/indexed_vcf
vep_fields: vep_to_table_fields
tsv: variants_to_table/variants_tsv
out: [annotated_variants_tsv]