#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment and somatic variant detection"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_cram_name:
type: string?
default: 'tumor.cram'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_cram_name:
type: string?
default: 'normal.cram'
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]
bait_intervals:
type: File
target_intervals:
type: File
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
qc_minimum_mapping_quality:
type: int?
default: 0
qc_minimum_base_quality:
type: int?
default: 0
interval_list:
type: File
cosmic_vcf:
type: File?
secondaryFiles: [.tbi]
panel_of_normals_vcf:
type: File?
secondaryFiles: [.tbi]
strelka_cpu_reserved:
type: int?
default: 8
mutect_scatter_count:
type: int
mutect_artifact_detection_mode:
type: boolean
default: false
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: 0.05
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]
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"]
cle_vcf_filter:
type: boolean
default: false
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: [HGVSc,HGVSp]
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
outputs:
tumor_cram:
type: File
outputSource: tumor_alignment_and_qc/cram
tumor_mark_duplicates_metrics:
type: File
outputSource: tumor_alignment_and_qc/mark_duplicates_metrics
tumor_insert_size_metrics:
type: File
outputSource: tumor_alignment_and_qc/insert_size_metrics
tumor_alignment_summary_metrics:
type: File
outputSource: tumor_alignment_and_qc/alignment_summary_metrics
tumor_hs_metrics:
type: File
outputSource: tumor_alignment_and_qc/hs_metrics
tumor_per_target_coverage_metrics:
type: File[]
outputSource: tumor_alignment_and_qc/per_target_coverage_metrics
tumor_per_target_hs_metrics:
type: File[]
outputSource: tumor_alignment_and_qc/per_target_hs_metrics
tumor_per_base_coverage_metrics:
type: File[]
outputSource: tumor_alignment_and_qc/per_base_coverage_metrics
tumor_per_base_hs_metrics:
type: File[]
outputSource: tumor_alignment_and_qc/per_base_hs_metrics
tumor_summary_hs_metrics:
type: File[]
outputSource: tumor_alignment_and_qc/summary_hs_metrics
tumor_flagstats:
type: File
outputSource: tumor_alignment_and_qc/flagstats
tumor_verify_bam_id_metrics:
type: File
outputSource: tumor_alignment_and_qc/verify_bam_id_metrics
tumor_verify_bam_id_depth:
type: File
outputSource: tumor_alignment_and_qc/verify_bam_id_depth
normal_cram:
type: File
outputSource: normal_alignment_and_qc/cram
normal_mark_duplicates_metrics:
type: File
outputSource: normal_alignment_and_qc/mark_duplicates_metrics
normal_insert_size_metrics:
type: File
outputSource: normal_alignment_and_qc/insert_size_metrics
normal_alignment_summary_metrics:
type: File
outputSource: normal_alignment_and_qc/alignment_summary_metrics
normal_hs_metrics:
type: File
outputSource: normal_alignment_and_qc/hs_metrics
normal_per_target_coverage_metrics:
type: File[]
outputSource: normal_alignment_and_qc/per_target_coverage_metrics
normal_per_target_hs_metrics:
type: File[]
outputSource: normal_alignment_and_qc/per_target_hs_metrics
normal_per_base_coverage_metrics:
type: File[]
outputSource: normal_alignment_and_qc/per_base_coverage_metrics
normal_per_base_hs_metrics:
type: File[]
outputSource: normal_alignment_and_qc/per_base_hs_metrics
normal_summary_hs_metrics:
type: File[]
outputSource: normal_alignment_and_qc/summary_hs_metrics
normal_flagstats:
type: File
outputSource: normal_alignment_and_qc/flagstats
normal_verify_bam_id_metrics:
type: File
outputSource: normal_alignment_and_qc/verify_bam_id_metrics
normal_verify_bam_id_depth:
type: File
outputSource: normal_alignment_and_qc/verify_bam_id_depth
mutect_unfiltered_vcf:
type: File
outputSource: detect_variants/mutect_unfiltered_vcf
secondaryFiles: [.tbi]
mutect_filtered_vcf:
type: File
outputSource: detect_variants/mutect_filtered_vcf
secondaryFiles: [.tbi]
strelka_unfiltered_vcf:
type: File
outputSource: detect_variants/strelka_unfiltered_vcf
secondaryFiles: [.tbi]
strelka_filtered_vcf:
type: File
outputSource: detect_variants/strelka_filtered_vcf
secondaryFiles: [.tbi]
varscan_unfiltered_vcf:
type: File
outputSource: detect_variants/varscan_unfiltered_vcf
secondaryFiles: [.tbi]
varscan_filtered_vcf:
type: File
outputSource: detect_variants/varscan_filtered_vcf
secondaryFiles: [.tbi]
pindel_unfiltered_vcf:
type: File
outputSource: detect_variants/pindel_unfiltered_vcf
secondaryFiles: [.tbi]
pindel_filtered_vcf:
type: File
outputSource: detect_variants/pindel_filtered_vcf
secondaryFiles: [.tbi]
docm_unfiltered_vcf:
type: File
outputSource: detect_variants/docm_unfiltered_vcf
docm_filtered_vcf:
type: File
outputSource: detect_variants/docm_filtered_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: detect_variants/final_vcf
secondaryFiles: [.tbi]
final_filtered_vcf:
type: File
outputSource: detect_variants/final_filtered_vcf
secondaryFiles: [.tbi]
final_tsv:
type: File
outputSource: detect_variants/final_tsv
vep_summary:
type: File
outputSource: detect_variants/vep_summary
tumor_snv_bam_readcount_tsv:
type: File
outputSource: detect_variants/tumor_snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv:
type: File
outputSource: detect_variants/tumor_indel_bam_readcount_tsv
normal_snv_bam_readcount_tsv:
type: File
outputSource: detect_variants/normal_snv_bam_readcount_tsv
normal_indel_bam_readcount_tsv:
type: File
outputSource: detect_variants/normal_indel_bam_readcount_tsv
intervals_antitarget:
type: File?
outputSource: cnvkit/intervals_antitarget
intervals_target:
type: File?
outputSource: cnvkit/intervals_target
normal_antitarget_coverage:
type: File
outputSource: cnvkit/normal_antitarget_coverage
normal_target_coverage:
type: File
outputSource: cnvkit/normal_target_coverage
reference_coverage:
type: File?
outputSource: cnvkit/reference_coverage
cn_diagram:
type: File?
outputSource: cnvkit/cn_diagram
cn_scatter_plot:
type: File?
outputSource: cnvkit/cn_scatter_plot
tumor_antitarget_coverage:
type: File
outputSource: cnvkit/tumor_antitarget_coverage
tumor_target_coverage:
type: File
outputSource: cnvkit/tumor_target_coverage
tumor_bin_level_ratios:
type: File
outputSource: cnvkit/tumor_bin_level_ratios
tumor_segmented_ratios:
type: File
outputSource: cnvkit/tumor_segmented_ratios
steps:
tumor_alignment_and_qc:
run: exome_alignment.cwl
in:
reference: reference
bams: tumor_bams
readgroups: tumor_readgroups
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
final_name: tumor_cram_name
out:
[cram, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
normal_alignment_and_qc:
run: exome_alignment.cwl
in:
reference: reference
bams: normal_bams
readgroups: normal_readgroups
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
final_name: normal_cram_name
out:
[cram, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
detect_variants:
run: detect_variants.cwl
in:
reference: reference
tumor_cram: tumor_alignment_and_qc/cram
normal_cram: normal_alignment_and_qc/cram
interval_list: interval_list
dbsnp_vcf: dbsnp_vcf
cosmic_vcf: cosmic_vcf
panel_of_normals_vcf: panel_of_normals_vcf
strelka_exome_mode:
default: true
strelka_cpu_reserved: strelka_cpu_reserved
mutect_scatter_count: mutect_scatter_count
mutect_artifact_detection_mode: mutect_artifact_detection_mode
mutect_max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction
mutect_max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_count
varscan_strand_filter: varscan_strand_filter
varscan_min_coverage: varscan_min_coverage
varscan_min_var_freq: varscan_min_var_freq
varscan_p_value: varscan_p_value
varscan_max_normal_freq: varscan_max_normal_freq
pindel_insert_size: pindel_insert_size
docm_vcf: docm_vcf
vep_cache_dir: vep_cache_dir
synonyms_file: synonyms_file
annotate_coding_only: annotate_coding_only
vep_pick: vep_pick
cle_vcf_filter: cle_vcf_filter
variants_to_table_fields: variants_to_table_fields
variants_to_table_genotype_fields: variants_to_table_genotype_fields
vep_to_table_fields: vep_to_table_fields
custom_gnomad_vcf: custom_gnomad_vcf
custom_clinvar_vcf: custom_clinvar_vcf
out:
[mutect_unfiltered_vcf, mutect_filtered_vcf, strelka_unfiltered_vcf, strelka_filtered_vcf, varscan_unfiltered_vcf, varscan_filtered_vcf, pindel_unfiltered_vcf, pindel_filtered_vcf, docm_unfiltered_vcf, docm_filtered_vcf, final_vcf, final_filtered_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv, normal_snv_bam_readcount_tsv, normal_indel_bam_readcount_tsv]
cnvkit:
run: ../subworkflows/cram_to_cnvkit.cwl
in:
normal_cram: tumor_alignment_and_qc/cram
tumor_cram: normal_alignment_and_qc/cram
reference: reference
bait_intervals: bait_intervals
out:
[intervals_antitarget, intervals_target, normal_antitarget_coverage, normal_target_coverage, reference_coverage, cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios]