/
pindel_cat.cwl
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/
pindel_cat.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Per-region pindel"
requirements:
- class: MultipleInputFeatureRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
type: File
secondaryFiles: ["^.bai"]
normal_bam:
type: File
secondaryFiles: ["^.bai"]
region_file:
type: File
insert_size:
type: int
default: 400
tumor_sample_name:
type: string
normal_sample_name:
type: string
outputs:
per_region_pindel_out:
type: File
outputSource: cat/pindel_out
steps:
pindel:
run: ../tools/pindel.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
insert_size: insert_size
region_file: region_file
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[deletions, insertions, tandems, long_insertions, inversions]
cat:
run: ../tools/cat_out.cwl
in:
pindel_outs: [pindel/deletions, pindel/insertions, pindel/tandems, pindel/long_insertions, pindel/inversions]
out:
[pindel_out]