Workflow: Subworkflow to allow calling different SV callers which require bam files as inputs

Fetched 2020-01-29 15:01:08 GMT
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Inputs

ID Type Title Doc
cnvkit_diagram Boolean (Optional)
merge_same_strand Boolean
sv_paired_count Integer (Optional)
manta_non_wgs Boolean (Optional)
cnvkit_male_reference Boolean (Optional)
snps_vcf File (Optional)
smoove_exclude_regions File (Optional)
bam File
reference String
cnv_filter_min_size Integer (Optional)
merge_estimate_sv_distance Boolean
manta_output_contigs Boolean (Optional)
merge_max_distance Integer
cnv_duplication_depth Double (Optional)
cnv_deletion_depth Double (Optional)
sv_alt_abundance_percentage Double (Optional)
manta_call_regions File (Optional)
cnvkit_scatter_plot Boolean (Optional)
sv_split_count Integer (Optional)
cnvkit_vcf_name String (Optional)
merge_same_type Boolean
cnvkit_reference_cnn File
cnvkit_drop_low_coverage Boolean (Optional)
merge_min_sv_size Integer
cnvkit_method String (Optional)
genome_build String
merge_min_svs Integer

Steps

ID Runs Label Doc
run_smoove
../tools/smoove.cwl (CommandLineTool)
Run Smoove v0.1.6
run_cnvnator
../tools/cnvnator.cwl (CommandLineTool)
Run CNVnator to calculate copy number variations in WGS samples
run_cnvnator_raw_bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
run_cnvkit_raw_index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
run_manta
../tools/manta_somatic.cwl (CommandLineTool)
Set up and execute manta
run_manta_filter Filter single sample sv vcf from paired read callers(Manta/Smoove)
run_cnvkit_filter Filter single sample sv vcf from depth callers(cnvkit/cnvnator)
run_cnvnator_filter Filter single sample sv vcf from depth callers(cnvkit/cnvnator)
run_merge
merge_svs.cwl (Workflow)
Merge, annotate, and generate a TSV for SVs
run_smoove_filter Filter single sample sv vcf from paired read callers(Manta/Smoove)
run_cnvkit_raw_bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
run_cnvnator_raw_index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
run_cnvkit Subworkflow that runs cnvkit in single sample mode and returns a vcf file

Outputs

ID Type Label Doc
smoove_output_variants File
tumor_antitarget_coverage File
manta_somatic_variants File (Optional)
cnvkit_filtered_vcf File
smoove_filtered_vcf File
bcftools_merged_filtered_annotated_tsv File
cnvnator_root File
tumor_target_coverage File
survivor_merged_annotated_tsv File
manta_filtered_vcf File
bcftools_merged_annotated_tsv File
survivor_merged_vcf File
tumor_segmented_ratios File
cn_scatter_plot File (Optional)
cnvnator_vcf File
manta_small_candidates File
cnvnator_filtered_vcf File
bcftools_merged_vcf File
manta_tumor_only_variants File (Optional)
cnvkit_vcf File
manta_diploid_variants File (Optional)
manta_all_candidates File
cnvnator_cn_file File
cn_diagram File (Optional)
tumor_bin_level_ratios File
Permalink: https://w3id.org/cwl/view/git/f615832615c3b41728df8e47b72ef11e37e6a9e5/definitions/subworkflows/single_sample_sv_callers.cwl