forked from genome/analysis-workflows
/
workflow.cwl
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workflow.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
inputs:
reference:
type: File
secondaryFiles: [".fai"]
tumor_bam:
type: File
secondaryFiles: ["^.bai"]
normal_bam:
type: File
secondaryFiles: ["^.bai"]
interval_list:
type: File
insert_size:
type: int
default: 400
outputs:
merged_vcf:
type: File
outputSource: index_filtered/indexed_vcf
secondaryFiles: [".tbi"]
steps:
get_tumor_bam_index:
run: get_bam_index.cwl
in:
bam: tumor_bam
out:
[bam_index]
get_normal_bam_index:
run: get_bam_index.cwl
in:
bam: normal_bam
out:
[bam_index]
get_chromosome_list:
run: get_chromosome_list.cwl
in:
interval_list: interval_list
out:
[chromosome_list]
pindel_cat:
scatter: chromosome
run: pindel_cat.cwl
in:
reference: reference
tumor_bam: tumor_bam
normal_bam: normal_bam
tumor_bam_index: [get_tumor_bam_index/bam_index]
normal_bam_index: [get_normal_bam_index/bam_index]
chromosome: [get_chromosome_list/chromosome_list]
insert_size: insert_size
out:
[per_chromosome_pindel_out]
cat_all:
run: cat_all.cwl
in:
chromosome_pindel_outs: [pindel_cat/per_chromosome_pindel_out]
out:
[all_chromosome_pindel_out]
grep:
run: grep.cwl
in:
pindel_output: cat_all/all_chromosome_pindel_out
out:
[pindel_head]
somaticfilter:
run: somaticfilter.cwl
in:
reference: reference
pindel_output_summary: grep/pindel_head
out:
[vcf]
bgzip:
run: ../detect_variants/bgzip.cwl
in:
file: somaticfilter/vcf
out:
[bgzipped_file]
index:
run: ../detect_variants/index.cwl
in:
vcf: bgzip/bgzipped_file
out:
[indexed_vcf]
region_filter:
run: ../detect_variants/select_variants.cwl
in:
reference: reference
vcf: index/indexed_vcf
interval_list: interval_list
out:
[filtered_vcf]
index_filtered:
run: ../detect_variants/index.cwl
in:
vcf: region_filter/filtered_vcf
out:
[indexed_vcf]