-
Notifications
You must be signed in to change notification settings - Fork 57
/
gatk_haplotypecaller_iterator.cwl
48 lines (46 loc) · 1.13 KB
/
gatk_haplotypecaller_iterator.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "scatter GATK HaplotypeCaller over intervals"
requirements:
- class: ScatterFeatureRequirement
inputs:
reference:
type: string
cram:
type: File
secondaryFiles: [^.crai]
emit_reference_confidence:
type: string
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
dbsnp_vcf:
type: File?
secondaryFiles: [.tbi]
contamination_fraction:
type: string?
outputs:
gvcf:
type: File[]
outputSource: haplotype_caller/gvcf
secondaryFiles: [.tbi]
steps:
haplotype_caller:
scatter: [intervals]
run: gatk_haplotypecaller.cwl
in:
reference: reference
cram: cram
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
dbsnp_vcf: dbsnp_vcf
contamination_fraction: contamination_fraction
out:
[gvcf]