Workflow: pindel parallel workflow

Fetched 2023-01-13 12:01:33 GMT
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Workflow as SVG
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  • Default Values
  • Nested Workflows
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  • Inputs/Outputs

Inputs

ID Type Title Doc
reference String
tumor_bam File
normal_bam File
insert_size Integer
interval_list File
scatter_count Integer

Steps

ID Runs Label Doc
bgzip
../tools/bgzip.cwl (CommandLineTool)
bgzip VCF
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
filter
fp_filter.cwl (Workflow)
fp_filter workflow
cat_all
../tools/cat_all.cwl (CommandLineTool)
reindex
../tools/index_vcf.cwl (CommandLineTool)
vcf index
pindel_cat
pindel_cat.cwl (Workflow)
Per-region pindel
somaticfilter
../tools/pindel_somatic_filter.cwl (CommandLineTool)
pindel somatic filter v1
remove_end_tags
../tools/remove_end_tags.cwl (CommandLineTool)
remove END INFO tags
split_interval_list_to_bed
../tools/split_interval_list_to_bed.cwl (CommandLineTool)

Outputs

ID Type Label Doc
filtered_vcf File
unfiltered_vcf File
Permalink: https://w3id.org/cwl/view/git/ec5355f335852e51c6938809c16ea1d230a3f983/definitions/subworkflows/pindel.cwl