/
vqsr-flow.cwl
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vqsr-flow.cwl
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cwlVersion: v1.0
class: Workflow
doc: "run vqsr flow, including vqsr rcal, vqsr apply and plot"
requirements:
- class: MultipleInputFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: ResourceRequirement
coresMin: $(inputs.threads)
inputs:
reference:
type: [string, File]
secondaryFiles:
- .fai
var_type:
type: ["null", string]
input_vcf:
type: [string, File]
secondaryFiles:
- .tbi
# require resource and resource_param in pairs
resources:
type:
type: array
items:
- type: record
name: resource
fields:
- name: resource
type: [string, File]
inputBinding:
prefix: --resource
- name: resource_param
type: string
inputBinding:
prefix: --resource_param
annotation:
type: string[]
aggregate_data:
type:
- "null"
- type: array
items: [string, File]
secondaryFiles:
- .tbi
max_gaussians:
type: ["null", int]
max_neg_gaussians:
type: ["null", int]
max_iter:
type: ["null", int]
max_mq:
type: ["null", double]
srand:
type: ["null", long]
sensitivity:
type: ["null", double]
output_file:
type: string
threads:
type: ["null", int]
inputBinding:
prefix: -t
position: 10
advanced_options:
type:
- "null"
- type: record
fields:
- name: vqsr_recal
type:
- "null"
- type: array
items: string
- name: vqsr_apply
type:
- "null"
- type: array
items: string
outputs:
output:
type: File
outputSource: vqsr_apply/output
plot_output:
type: ["null", File]
outputSource: plot/output
tranches_output:
type: File
outputSource: vqsr_recal/tranches_output
steps:
vqsr_recal:
in:
input_vcf: input_vcf
reference: reference
threads: threads
var_type: var_type
resources: resources
annotation: annotation
aggregate_data: aggregate_data
max_gaussians: max_gaussians
max_neg_gaussians: max_neg_gaussians
max_iter: max_iter
max_mq: max_mq
srand: srand
plot_file:
source: output_file
valueFrom: $(self).plot
tranches_file:
source: output_file
valueFrom: $(self).tranches
output_file:
source: output_file
valueFrom: $(self).recal.gz
advanced_options:
source: advanced_options
valueFrom: |
${ return self ? self.vqsr_recal : []; }
out: [output, tranches_output, plot_output]
run: ../algo/vqsr-recal.cwl
vqsr_apply:
in:
input_vcf: input_vcf
reference: reference
var_type: var_type
threas: threads
sensitivity: sensitivity
recal: vqsr_recal/output
tranches_file: vqsr_recal/tranches_output
output_file: output_file
advanced_options:
source: advanced_options
valueFrom: |
${ return self ? self.vqsr_apply : []; }
out: [output]
run: ../algo/vqsr-apply.cwl
plot:
in:
output_file:
source: output_file
valueFrom: $(self).pdf
input: vqsr_recal/plot_output
tranches_file: vqsr_recal/tranches_output
fun:
valueFrom: ${ return "vqsr"; }
out: [output]
run: ../algo/plot.cwl