/
downsampled_alignment.cwl
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downsampled_alignment.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "downsample unaligned BAM and align"
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
bams:
type: File[]
readgroups:
type: string[]
reference:
type: string
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
downsample_probability:
type: float
outputs:
bam:
type: File
outputSource: align_workflow/final_bam
secondaryFiles: [.bai, ^.bai]
mark_duplicates_metrics_file:
type: File
outputSource: align_workflow/mark_duplicates_metrics_file
steps:
downsample:
scatter: [sam]
scatterMethod: dotproduct
run: ../tools/downsample.cwl
in:
sam: bams
probability: downsample_probability
reference: reference
out:
[downsampled_sam]
align_workflow:
run: bam_to_bqsr.cwl
in:
bams: downsample/downsampled_sam
readgroups: readgroups
reference: reference
dbsnp_vcf: dbsnp_vcf
mills: mills
known_indels: known_indels
out:
[final_bam,mark_duplicates_metrics_file]