Workflow: Varscan Workflow

Fetched 2023-01-09 22:30:53 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs strand_filter strand_filter varscan varscan v2.4.2 germline strand_filter->varscan strand_filter sample_name sample_name filter fp_filter workflow sample_name->filter sample_name sample_name->varscan sample_name interval_list interval_list intervals_to_bed intervals_to_bed interval_list->intervals_to_bed interval_list max_normal_freq max_normal_freq min_reads min_reads min_reads->varscan min_reads min_var_freq min_var_freq min_var_freq->filter min_var_freq min_var_freq->varscan min_var_freq min_coverage min_coverage min_coverage->varscan min_coverage bam bam bam->filter bam bam->varscan bam p_value p_value p_value->varscan p_value reference reference reference->filter reference reference->varscan reference unfiltered_vcf unfiltered_vcf filtered_vcf filtered_vcf intervals_to_bed->varscan roi_bed filter->unfiltered_vcf filter->filtered_vcf bgzip_and_index bgzip and index VCF varscan->bgzip_and_index vcf bgzip_and_index->filter vcf
Workflow as SVG
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Inputs

ID Type Title Doc
bam File
p_value Float (Optional)
min_reads Integer (Optional)
reference File
sample_name String
min_coverage Integer (Optional)
min_var_freq Float (Optional)
interval_list File
strand_filter Integer (Optional)
max_normal_freq Float (Optional)

Steps

ID Runs Label Doc
filter
fp_filter.cwl (Workflow)
fp_filter workflow
varscan
../tools/varscan_germline.cwl (CommandLineTool)
varscan v2.4.2 germline
bgzip_and_index
bgzip_and_index.cwl (Workflow)
bgzip and index VCF
intervals_to_bed
../tools/intervals_to_bed.cwl (CommandLineTool)

Outputs

ID Type Label Doc
filtered_vcf File
unfiltered_vcf File
Permalink: https://w3id.org/cwl/view/git/b8000c793d6e7ce4d690406c4f914c5c62acd51f/definitions/subworkflows/varscan_germline.cwl