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detect_variants_mouse.cwl
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detect_variants_mouse.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
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
type: File
secondaryFiles: [.bai,^.bai]
normal_bam:
type: File
secondaryFiles: [.bai,^.bai]
interval_list:
type: File
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
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
vep_cache_dir:
type:
- string
- Directory
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?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
vep_plugins:
type: string[]
default: [Downstream, Wildtype]
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]
variants_to_table_genotype_fields:
type: string[]
default: [GT,AD]
vep_to_table_fields:
type: string[]
default: []
tumor_sample_name:
type: string
normal_sample_name:
type: string
outputs:
mutect_unfiltered_vcf:
type: File
outputSource: mutect/unfiltered_vcf
secondaryFiles: [.tbi]
mutect_filtered_vcf:
type: File
outputSource: mutect/filtered_vcf
secondaryFiles: [.tbi]
strelka_unfiltered_vcf:
type: File
outputSource: strelka/unfiltered_vcf
secondaryFiles: [.tbi]
strelka_filtered_vcf:
type: File
outputSource: strelka/filtered_vcf
secondaryFiles: [.tbi]
varscan_unfiltered_vcf:
type: File
outputSource: varscan/unfiltered_vcf
secondaryFiles: [.tbi]
varscan_filtered_vcf:
type: File
outputSource: varscan/filtered_vcf
secondaryFiles: [.tbi]
pindel_unfiltered_vcf:
type: File
outputSource: pindel/unfiltered_vcf
secondaryFiles: [.tbi]
pindel_filtered_vcf:
type: File
outputSource: pindel/filtered_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: index/indexed_vcf
secondaryFiles: [.tbi]
final_filtered_vcf:
type: File
outputSource: annotated_filter_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
scatter_count: mutect_scatter_count
tumor_sample_name: tumor_sample_name
out:
[unfiltered_vcf, filtered_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
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[unfiltered_vcf, filtered_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
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[unfiltered_vcf, filtered_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
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[unfiltered_vcf, filtered_vcf]
combine:
run: ../tools/combine_variants.cwl
in:
reference: reference
mutect_vcf: mutect/filtered_vcf
strelka_vcf: strelka/filtered_vcf
varscan_vcf: varscan/filtered_vcf
pindel_vcf: pindel/filtered_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]
annotate_variants:
run: ../tools/vep.cwl
in:
vcf: decompose_index/indexed_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
pick: vep_pick
plugins: vep_plugins
out:
[annotated_vcf, vep_summary]
tumor_bam_readcount:
run: ../tools/bam_readcount.cwl
in:
vcf: annotate_variants/annotated_vcf
sample: tumor_sample_name
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: normal_sample_name
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: tumor_sample_name
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: normal_sample_name
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]
filter_vcf:
run: ../subworkflows/filter_vcf_mouse.cwl
in:
vcf: index/indexed_vcf
filter_mapq0_threshold: filter_mapq0_threshold
filter_somatic_llr_threshold: filter_somatic_llr_threshold
filter_minimum_depth: filter_minimum_depth
tumor_bam: tumor_bam
do_cle_vcf_filter: cle_vcf_filter
reference: reference
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[filtered_vcf]
annotated_filter_bgzip:
run: ../tools/bgzip.cwl
in:
file: filter_vcf/filtered_vcf
out:
[bgzipped_file]
annotated_filter_index:
run: ../tools/index_vcf.cwl
in:
vcf: annotated_filter_bgzip/bgzipped_file
out:
[indexed_vcf]
variants_to_table:
run: ../tools/variants_to_table.cwl
in:
reference: reference
vcf: annotated_filter_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: annotated_filter_index/indexed_vcf
vep_fields: vep_to_table_fields
tsv: variants_to_table/variants_tsv
out: [annotated_variants_tsv]