Workflow: Run pindel on provided region

Fetched 2023-01-04 10:01:24 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
ref_name String (Optional)
reference String
tumor_bam File
normal_bam File
insert_size Integer
output_name String (Optional)
region_file File
tumor_sample_name String
normal_sample_name String

Steps

ID Runs Label Doc
cat
../tools/cat_out.cwl (CommandLineTool)
index
../tools/index_vcf.cwl (CommandLineTool)
vcf index
pindel2vcf
../tools/pindel2vcf.cwl (CommandLineTool)
pindel v0.2.5b8
pindel_region
../tools/pindel.cwl (CommandLineTool)
pindel v0.2.5b8
fix_vcf_header
../tools/fix_vcf_header.cwl (CommandLineTool)
fix vcf header
remove_end_tags
../tools/remove_end_tags.cwl (CommandLineTool)
remove END INFO tags

Outputs

ID Type Label Doc
pindel_region_vcf File
Permalink: https://w3id.org/cwl/view/git/9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f/definitions/subworkflows/pindel_region.cwl