Workflow: mutect parallel workflow

Fetched 2023-01-10 00:56:17 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs max_alt_allele_in_normal_fraction max_alt_allele_in_normal_fraction mutect mutect2 (GATK 3.6) max_alt_allele_in_normal_fraction->mutect max_alt_allele_in_normal_fraction cosmic_vcf cosmic_vcf cosmic_vcf->mutect cosmic_vcf max_alt_alleles_in_normal_count max_alt_alleles_in_normal_count max_alt_alleles_in_normal_count->mutect max_alt_alleles_in_normal_count dbsnp_vcf dbsnp_vcf dbsnp_vcf->mutect dbsnp_vcf reference reference reference->mutect reference filter fp_filter workflow reference->filter reference artifact_detection_mode artifact_detection_mode artifact_detection_mode->mutect artifact_detection_mode normal_cram normal_cram normal_cram->mutect normal_cram scatter_count scatter_count split_interval_list split_interval_list scatter_count->split_interval_list scatter_count interval_list interval_list interval_list->split_interval_list interval_list panel_of_normals_vcf panel_of_normals_vcf panel_of_normals_vcf->mutect panel_of_normals_vcf tumor_cram tumor_cram tumor_cram->mutect tumor_cram tumor_cram->filter cram unfiltered_vcf unfiltered_vcf filtered_vcf filtered_vcf merge vcf merge mutect->merge vcfs index vcf index merge->index vcf index->filter vcf split_interval_list->mutect interval_list filter->unfiltered_vcf filter->filtered_vcf
Workflow as SVG
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Inputs

ID Type Title Doc
dbsnp_vcf File (Optional)
reference String
cosmic_vcf File (Optional)
tumor_cram File
normal_cram File (Optional)
interval_list File
scatter_count Integer
panel_of_normals_vcf File (Optional)
artifact_detection_mode Boolean
max_alt_alleles_in_normal_count Integer (Optional)
max_alt_allele_in_normal_fraction Float (Optional)

Steps

ID Runs Label Doc
index
../detect_variants/index.cwl (CommandLineTool)
vcf index
merge
../detect_variants/merge.cwl (CommandLineTool)
vcf merge
filter fp_filter workflow
mutect
mutect.cwl (CommandLineTool)
mutect2 (GATK 3.6)
split_interval_list
../detect_variants/split_interval_list.cwl (CommandLineTool)

Outputs

ID Type Label Doc
filtered_vcf File
unfiltered_vcf File
html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/e4c851d65f460e8f48ca184120044fce72cb2433/mutect/workflow.cwl