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

This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
bam	File
reference	String
cnvkit_method	String (Optional)
manta_non_wgs	Boolean (Optional)
merge_min_svs	Integer
cnvkit_diagram	Boolean (Optional)
cnvkit_vcf_name	String (Optional)
merge_same_type	Boolean
merge_min_sv_size	Integer
merge_same_strand	Boolean
manta_call_regions	File (Optional)
merge_max_distance	Integer
cnvkit_scatter_plot	Boolean (Optional)
cnvkit_reference_cnn	File
manta_output_contigs	Boolean (Optional)
merge_sv_pop_freq_db	File
cnvkit_male_reference	Boolean (Optional)
smoove_exclude_regions	File (Optional)
cnvkit_drop_low_coverage	Boolean (Optional)
merge_estimate_sv_distance	Boolean

ID	Runs	Label
run_manta	../tools/manta_somatic.cwl (CommandLineTool)	Set up and execute manta
run_merge	merge_svs.cwl (Workflow)	merge and annotate svs with population allele freq
run_cnvkit	cnvkit_single_sample.cwl (Workflow)	Subworkflow that runs cnvkit in single sample mode and returns a vcf file
run_smoove	../tools/smoove.cwl (CommandLineTool)	Run Smoove v0.1.6

ID	Type	Label	Doc
cn_diagram	File (Optional)
cnvkit_vcf	File
cn_scatter_plot	File (Optional)
manta_all_candidates	File
merged_annotated_svs	File
tumor_target_coverage	File
manta_diploid_variants	File (Optional)
manta_small_candidates	File
manta_somatic_variants	File (Optional)
smoove_output_variants	File
tumor_bin_level_ratios	File
tumor_segmented_ratios	File
manta_tumor_only_variants	File (Optional)
tumor_antitarget_coverage	File