Workflow: Run pindel on provided region

Fetched 2023-01-10 00:08:35 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs insert_size insert_size pindel_region pindel v0.2.5b8 insert_size->pindel_region insert_size output_name output_name pindel2vcf pindel v0.2.5b8 output_name->pindel2vcf output_name ref_name ref_name ref_name->pindel2vcf ref_name normal_sample_name normal_sample_name normal_sample_name->pindel_region normal_sample_name normal_bam normal_bam normal_bam->pindel_region normal_bam reference reference reference->pindel2vcf reference reference->pindel_region reference tumor_sample_name tumor_sample_name tumor_sample_name->pindel_region tumor_sample_name region_file region_file region_file->pindel_region region_file tumor_bam tumor_bam tumor_bam->pindel_region tumor_bam pindel_region_vcf pindel_region_vcf fix_vcf_header fix vcf header remove_end_tags remove END INFO tags fix_vcf_header->remove_end_tags vcf index vcf index remove_end_tags->index vcf cat cat cat->pindel2vcf pindel_out pindel2vcf->fix_vcf_header vcf index->pindel_region_vcf pindel_region->cat pindel_outs pindel_region->cat pindel_outs pindel_region->cat pindel_outs pindel_region->cat pindel_outs pindel_region->cat pindel_outs
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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/ecac0fda44df3a8f25ddfbb3e7a023fcbe4cbd0f/definitions/subworkflows/pindel_region.cwl