subworkflows_single_sample_sv_callers.cwl

Documentation for single_sample_sv_callers.cwl

This page is auto-generated. Do not edit.

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

Name	Type	Secondary Files
bam	File	['.bai', '^.bai']
reference	['string', 'File']	['.fai', '^.dict']
cnvkit_diagram	boolean?
cnvkit_drop_low_coverage	boolean?
cnvkit_method	['null', {'type': 'enum', 'symbols': ['hybrid', 'amplicon', 'wgs']}]
cnvkit_reference_cnn	File?
cnvkit_scatter_plot	boolean?
cnvkit_male_reference	boolean?
cnvkit_vcf_name	string?
manta_call_regions	File?	['.tbi']
manta_non_wgs	boolean?
manta_output_contigs	boolean?
merge_max_distance	int
merge_min_svs	int
merge_same_type	boolean
merge_same_strand	boolean
merge_estimate_sv_distance	boolean
merge_min_sv_size	int
smoove_exclude_regions	File?
snps_vcf	File?
genome_build	string
sv_alt_abundance_percentage	double?
sv_paired_count	int?
sv_split_count	int?
cnv_deletion_depth	double?
cnv_duplication_depth	double?
cnv_filter_min_size	int?
blocklist_bedpe	File?

Name	Label	Description	Type	Secondary Files
cn_diagram			File?
cn_scatter_plot			File?
tumor_antitarget_coverage			File
tumor_target_coverage			File
tumor_bin_level_ratios			File
tumor_segmented_ratios			File
cnvkit_filtered_vcf			File
cnvkit_vcf			File
cnvnator_cn_file			File
cnvnator_filtered_vcf			File
cnvnator_root			File
cnvnator_vcf			File
manta_diploid_variants			File?
manta_filtered_vcf			File
manta_somatic_variants			File?
manta_all_candidates			File
manta_small_candidates			File
manta_tumor_only_variants			File?
smoove_output_variants			File
smoove_filtered_vcf			File
survivor_merged_vcf			File
survivor_merged_annotated_tsv			File
bcftools_merged_vcf			File
bcftools_merged_annotated_tsv			File
bcftools_merged_filtered_annotated_tsv			File

Name	CWL Run
run_cnvkit	subworkflows/cnvkit_single_sample.cwl
run_cnvkit_raw_bgzip	tools/bgzip.cwl
run_cnvkit_raw_index	tools/index_vcf.cwl
run_cnvkit_filter	subworkflows/sv_depth_caller_filter.cwl
run_cnvnator	tools/cnvnator.cwl
run_cnvnator_raw_bgzip	tools/bgzip.cwl
run_cnvnator_raw_index	tools/index_vcf.cwl
run_cnvnator_filter	subworkflows/sv_depth_caller_filter.cwl
run_manta	tools/manta_somatic.cwl
run_manta_filter	subworkflows/sv_paired_read_caller_filter.cwl
run_smoove	tools/smoove.cwl
run_smoove_filter	subworkflows/sv_paired_read_caller_filter.cwl
run_merge	subworkflows/merge_svs.cwl