Workflow: Detect Docm variants

Fetched 2023-01-11 05:02:46 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
docm_vcf File
reference File
tumor_bam File
normal_bam File
interval_list File
filter_docm_variants Boolean

Steps

ID Runs Label Doc
bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
bgzip2
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
index2
../tools/index_vcf.cwl (CommandLineTool)
vcf index
decompose
../tools/vt_decompose.cwl (CommandLineTool)
run vt decompose
docm_filter
../tools/filter_vcf_docm.cwl (CommandLineTool)
Filter variants from the DoCM detector
GATK_haplotype_caller
../tools/docm_gatk_haplotype_caller.cwl (CommandLineTool)
HaplotypeCaller (GATK4)

Outputs

ID Type Label Doc
docm_variants_vcf File
Permalink: https://w3id.org/cwl/view/git/97572e3a088d79f6a4166385f79e79ea77b11470/definitions/subworkflows/docm_cle.cwl