/
pindel.cwl
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/
pindel.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "pindel parallel workflow"
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
tumor_bam:
type: File
secondaryFiles: [.bai, ^.bai]
normal_bam:
type: File
secondaryFiles: [^.bai]
interval_list:
type: File
insert_size:
type: int
default: 400
scatter_count:
type: int
default: 50
tumor_sample_name:
type: string
normal_sample_name:
type: string
outputs:
unfiltered_vcf:
type: File
outputSource: filter/unfiltered_vcf
secondaryFiles: [".tbi"]
filtered_vcf:
type: File
outputSource: filter/filtered_vcf
secondaryFiles: [".tbi"]
steps:
split_interval_list_to_bed:
run: ../tools/split_interval_list_to_bed.cwl
in:
interval_list: interval_list
scatter_count: scatter_count
out:
[split_beds]
pindel_cat:
scatter: region_file
run: pindel_cat.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
region_file: split_interval_list_to_bed/split_beds
insert_size: insert_size
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
out:
[per_region_pindel_out]
cat_all:
run: ../tools/cat_all.cwl
in:
region_pindel_outs: pindel_cat/per_region_pindel_out
out:
[all_region_pindel_head]
somaticfilter:
run: ../tools/pindel_somatic_filter.cwl
in:
reference: reference
pindel_output_summary: cat_all/all_region_pindel_head
out:
[vcf]
bgzip:
run: ../tools/bgzip.cwl
in:
file: somaticfilter/vcf
out:
[bgzipped_file]
index:
run: ../tools/index_vcf.cwl
in:
vcf: bgzip/bgzipped_file
out:
[indexed_vcf]
remove_end_tags:
run: ../tools/remove_end_tags.cwl
in:
vcf: index/indexed_vcf
out:
[processed_vcf]
reindex:
run: ../tools/index_vcf.cwl
in:
vcf: remove_end_tags/processed_vcf
out:
[indexed_vcf]
filter:
run: fp_filter.cwl
in:
reference: reference
bam: tumor_bam
vcf: reindex/indexed_vcf
variant_caller:
valueFrom: "pindel"
sample_name: tumor_sample_name
out:
[unfiltered_vcf, filtered_vcf]