/
pindel_region.cwl
79 lines (78 loc) · 2.04 KB
/
pindel_region.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Run pindel on provided region"
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type: string
tumor_bam:
type: File
secondaryFiles: ["^.bai"]
normal_bam:
type: File
secondaryFiles: ["^.bai"]
region_file:
type: File
insert_size:
type: int
default: 400
ref_name:
type: string?
default: "GRCh38DH"
output_name:
type: string?
default: "pindel.vcf"
outputs:
pindel_region_vcf:
type: File
outputSource: index/indexed_vcf
secondaryFiles: [".tbi"]
steps:
pindel_region:
run: ../tools/pindel.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
insert_size: insert_size
region_file: region_file
out:
[deletions, insertions, tandems, long_insertions, inversions]
cat:
run: ../tools/cat_out.cwl
in:
pindel_outs: [pindel_region/deletions, pindel_region/insertions, pindel_region/tandems, pindel_region/long_insertions, pindel_region/inversions]
out:
[pindel_out]
pindel2vcf:
run: ../tools/pindel2vcf.cwl
in:
pindel_out: cat/pindel_out
reference: reference
ref_name: ref_name
output_name: output_name
out:
[pindel_vcf]
fix_vcf_header:
run: ../tools/fix_vcf_header.cwl
in:
vcf: pindel2vcf/pindel_vcf
out:
[fixed_vcf]
remove_end_tags:
run: ../tools/remove_end_tags.cwl
in:
vcf: fix_vcf_header/fixed_vcf
out:
[processed_vcf]
index:
run: ../tools/index_vcf.cwl
in:
vcf: remove_end_tags/processed_vcf
out:
[indexed_vcf]