Workflow: Detect Docm variants

Fetched 2023-01-05 07:33:59 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs normal_bam normal_bam GATK_haplotype_caller HaplotypeCaller (GATK4) normal_bam->GATK_haplotype_caller normal_bam docm_filter Filter variants from the DoCM detector normal_bam->docm_filter normal_bam interval_list interval_list interval_list->GATK_haplotype_caller interval_list reference reference reference->GATK_haplotype_caller reference filter_docm_variants filter_docm_variants filter_docm_variants->docm_filter filter_docm_variants tumor_bam tumor_bam tumor_bam->GATK_haplotype_caller bam tumor_bam->docm_filter tumor_bam docm_vcf docm_vcf docm_vcf->GATK_haplotype_caller docm_vcf docm_variants_vcf docm_variants_vcf bgzip2 bgzip VCF index2 vcf index bgzip2->index2 vcf decompose run vt decompose decompose->docm_filter docm_raw_variants index2->docm_variants_vcf bgzip bgzip VCF GATK_haplotype_caller->bgzip file index vcf index bgzip->index vcf docm_filter->bgzip2 file index->decompose vcf
Workflow as SVG
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  • Inputs/Outputs

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/742dbafb5fb103d8578f48a0576c14dd8dae3b2a/definitions/subworkflows/docm_cle.cwl