subworkflows_vcf_eval_concordance.cwl

Documentation for vcf_eval_concordance.cwl

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Vcf concordance evaluation workflow

Name	Type	Secondary Files
reference	['string', 'File']	['.fai', '^.dict']
roi_bed	File
base_normal_cram	File	['^.crai']
base_tumor_cram	File	['^.crai']
base_vcf	File	['.tbi']
query_normal_cram	File	['^.crai']
query_tumor_cram	File	['^.crai']
query_vcf	File	['.tbi']
normal_sample_name	string?
tumor_sample_name	string?
output_dir	string

Name	Label	Description	Type	Secondary Files
output_directory			Directory

Name	CWL Run
base_normal_cram_to_bam_and_index	subworkflows/cram_to_bam_and_index.cwl
base_tumor_cram_to_bam_and_index	subworkflows/cram_to_bam_and_index.cwl
query_normal_cram_to_bam_and_index	subworkflows/cram_to_bam_and_index.cwl
query_tumor_cram_to_bam_and_index	subworkflows/cram_to_bam_and_index.cwl
base_vcf_pass	tools/select_variants.cwl
base_vcf_pass_roi	tools/bedtools_intersect.cwl
bgzip_and_index_base_pass_roi	subworkflows/bgzip_and_index.cwl
query_vcf_pass	tools/select_variants.cwl
query_vcf_pass_roi	tools/bedtools_intersect.cwl
bgzip_and_index_query_pass_roi	subworkflows/bgzip_and_index.cwl
combine_vcf	tools/combine_variants_concordance.cwl
base_normal_bam_readcount	tools/bam_readcount.cwl
base_tumor_bam_readcount	tools/bam_readcount.cwl
query_normal_bam_readcount	tools/bam_readcount.cwl
query_tumor_bam_readcount	tools/bam_readcount.cwl
sompy	tools/sompy.cwl
vaf_report	tools/eval_vaf_report.cwl
plot_output	tools/somatic_concordance_graph.cwl
gather_to_sub_directory	tools/gather_to_sub_directory.cwl