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single_sample_sv_callers.cwl
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single_sample_sv_callers.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Subworkflow to allow calling different SV callers which require bam files as inputs"
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
secondaryFiles: [.bai,^.bai]
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
cnvkit_diagram:
type: boolean?
cnvkit_drop_low_coverage:
type: boolean?
cnvkit_method:
type:
- "null"
- type: enum
symbols: ["hybrid", "amplicon", "wgs"]
cnvkit_reference_cnn:
type: File?
cnvkit_scatter_plot:
type: boolean?
cnvkit_male_reference:
type: boolean?
cnvkit_vcf_name:
type: string?
manta_call_regions:
type: File?
secondaryFiles: [.tbi]
manta_non_wgs:
type: boolean?
manta_output_contigs:
type: boolean?
merge_max_distance:
type: int
merge_min_svs:
type: int
merge_same_type:
type: boolean
merge_same_strand:
type: boolean
merge_estimate_sv_distance:
type: boolean
merge_min_sv_size:
type: int
smoove_exclude_regions:
type: File?
snps_vcf:
type: File?
genome_build:
type: string
sv_alt_abundance_percentage:
type: double?
sv_paired_count:
type: int?
sv_split_count:
type: int?
cnv_deletion_depth:
type: double?
cnv_duplication_depth:
type: double?
cnv_filter_min_size:
type: int?
blocklist_bedpe:
type: File?
outputs:
cn_diagram:
type: File?
outputSource: run_cnvkit/cn_diagram
cn_scatter_plot:
type: File?
outputSource: run_cnvkit/cn_scatter_plot
tumor_antitarget_coverage:
type: File
outputSource: run_cnvkit/tumor_antitarget_coverage
tumor_target_coverage:
type: File
outputSource: run_cnvkit/tumor_target_coverage
tumor_bin_level_ratios:
type: File
outputSource: run_cnvkit/tumor_bin_level_ratios
tumor_segmented_ratios:
type: File
outputSource: run_cnvkit/tumor_segmented_ratios
cnvkit_filtered_vcf:
type: File
outputSource: run_cnvkit_filter/filtered_vcf
cnvkit_vcf:
type: File
outputSource: run_cnvkit_raw_index/indexed_vcf
cnvnator_cn_file:
type: File
outputSource: run_cnvnator/cn_file
cnvnator_filtered_vcf:
type: File
outputSource: run_cnvnator_filter/filtered_vcf
cnvnator_root:
type: File
outputSource: run_cnvnator/root_file
cnvnator_vcf:
type: File
outputSource: run_cnvnator_raw_index/indexed_vcf
manta_diploid_variants:
type: File?
outputSource: run_manta/diploid_variants
manta_filtered_vcf:
type: File
outputSource: run_manta_filter/filtered_vcf
manta_somatic_variants:
type: File?
outputSource: run_manta/somatic_variants
manta_all_candidates:
type: File
outputSource: run_manta/all_candidates
manta_small_candidates:
type: File
outputSource: run_manta/small_candidates
manta_tumor_only_variants:
type: File?
outputSource: run_manta/tumor_only_variants
smoove_output_variants:
type: File
outputSource: run_smoove/output_vcf
smoove_filtered_vcf:
type: File
outputSource: run_smoove_filter/filtered_vcf
survivor_merged_vcf:
type: File
outputSource: run_merge/survivor_merged_sv_vcf
survivor_merged_annotated_tsv:
type: File
outputSource: run_merge/survivor_merged_annotated_tsv
bcftools_merged_vcf:
type: File
outputSource: run_merge/bcftools_merged_sv_vcf
bcftools_merged_annotated_tsv:
type: File
outputSource: run_merge/bcftools_merged_annotated_tsv
bcftools_merged_filtered_annotated_tsv:
type: File
outputSource: run_merge/bcftools_merged_filtered_annotated_tsv
steps:
run_cnvkit:
run: cnvkit_single_sample.cwl
in:
diagram: cnvkit_diagram
drop_low_coverage: cnvkit_drop_low_coverage
method: cnvkit_method
reference_cnn: cnvkit_reference_cnn
tumor_bam: bam
scatter_plot: cnvkit_scatter_plot
male_reference: cnvkit_male_reference
cnvkit_vcf_name: cnvkit_vcf_name
segment_filter:
default: "cn"
fasta_reference: reference
out:
[cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios, cnvkit_vcf]
run_cnvkit_raw_bgzip:
run: ../tools/bgzip.cwl
in:
file: run_cnvkit/cnvkit_vcf
out:
[bgzipped_file]
run_cnvkit_raw_index:
run: ../tools/index_vcf.cwl
in:
vcf: run_cnvkit_raw_bgzip/bgzipped_file
out:
[indexed_vcf]
run_cnvkit_filter:
run: sv_depth_caller_filter.cwl
in:
deletion_depth: cnv_deletion_depth
duplication_depth: cnv_duplication_depth
min_sv_size: cnv_filter_min_size
output_vcf_name:
default: "filtered_cnvkit.vcf"
sv_vcf: run_cnvkit/cnvkit_vcf
vcf_source:
default: "cnvkit"
out:
[filtered_vcf]
run_cnvnator:
run: ../tools/cnvnator.cwl
in:
bam: bam
reference: reference
sample_name:
default: "cnvnator"
out:
[vcf, root_file, cn_file]
run_cnvnator_raw_bgzip:
run: ../tools/bgzip.cwl
in:
file: run_cnvnator/vcf
out:
[bgzipped_file]
run_cnvnator_raw_index:
run: ../tools/index_vcf.cwl
in:
vcf: run_cnvnator_raw_bgzip/bgzipped_file
out:
[indexed_vcf]
run_cnvnator_filter:
run: sv_depth_caller_filter.cwl
in:
deletion_depth: cnv_deletion_depth
duplication_depth: cnv_duplication_depth
min_sv_size: cnv_filter_min_size
output_vcf_name:
default: "filtered_cnvnator.vcf"
sv_vcf: run_cnvnator/vcf
vcf_source:
default: "cnvnator"
out:
[filtered_vcf]
run_manta:
run: ../tools/manta_somatic.cwl
in:
call_regions: manta_call_regions
non_wgs: manta_non_wgs
output_contigs: manta_output_contigs
reference: reference
tumor_bam: bam
out:
[diploid_variants, somatic_variants, all_candidates, small_candidates, tumor_only_variants]
run_manta_filter:
run: sv_paired_read_caller_filter.cwl
in:
abundance_percentage: sv_alt_abundance_percentage
bam: bam
deletion_depth: cnv_deletion_depth
duplication_depth: cnv_duplication_depth
output_vcf_name:
default: "filtered_manta.vcf"
reference: reference
snps_vcf: snps_vcf
sv_paired_count: sv_paired_count
sv_split_count: sv_split_count
sv_vcf: run_manta/tumor_only_variants
vcf_source:
default: "manta"
out:
[filtered_vcf]
run_smoove:
run: ../tools/smoove.cwl
in:
bams:
source: [bam]
linkMerge: merge_flattened
exclude_regions: smoove_exclude_regions
reference: reference
out:
[output_vcf]
run_smoove_filter:
run: sv_paired_read_caller_filter.cwl
in:
abundance_percentage: sv_alt_abundance_percentage
bam: bam
deletion_depth: cnv_deletion_depth
duplication_depth: cnv_duplication_depth
output_vcf_name:
default: "filtered_smoove.vcf"
reference: reference
snps_vcf: snps_vcf
sv_paired_count: sv_paired_count
sv_split_count: sv_split_count
sv_vcf: run_smoove/output_vcf
vcf_source:
default: "smoove"
out:
[filtered_vcf]
run_merge:
run: merge_svs.cwl
in:
estimate_sv_distance: merge_estimate_sv_distance
genome_build: genome_build
max_distance_to_merge: merge_max_distance
minimum_sv_calls: merge_min_svs
minimum_sv_size: merge_min_sv_size
same_strand: merge_same_strand
same_type: merge_same_type
snps_vcf: snps_vcf
blocklist_bedpe: blocklist_bedpe
sv_vcfs:
source: [run_cnvkit_filter/filtered_vcf, run_cnvnator_filter/filtered_vcf, run_manta_filter/filtered_vcf, run_smoove_filter/filtered_vcf]
linkMerge: merge_flattened
out:
[bcftools_merged_sv_vcf, bcftools_merged_annotated_tsv, bcftools_merged_filtered_annotated_tsv, survivor_merged_sv_vcf, survivor_merged_annotated_tsv]