-
Notifications
You must be signed in to change notification settings - Fork 58
/
varscan_germline.cwl
84 lines (83 loc) · 2 KB
/
varscan_germline.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
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Varscan Workflow"
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type: string
bam:
type: File
secondaryFiles: [.bai, ^.bai]
interval_list:
type: File
strand_filter:
type: int?
default: 0
min_coverage:
type: int?
default: 8
min_var_freq:
type: float?
default: 0.1
min_reads:
type: int?
default: 2
p_value:
type: float?
default: 0.99
max_normal_freq:
type: float?
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:
intervals_to_bed:
run: ../tools/intervals_to_bed.cwl
in:
interval_list: interval_list
out:
[interval_bed]
varscan:
run: ../tools/varscan_germline.cwl
in:
reference: reference
bam: bam
roi_bed: intervals_to_bed/interval_bed
strand_filter: strand_filter
min_coverage: min_coverage
min_var_freq: min_var_freq
min_reads: min_reads
p_value: p_value
sample_name: sample_name
out:
[variants]
bgzip_and_index:
run: bgzip_and_index.cwl
in:
vcf: varscan/variants
out:
[indexed_vcf]
filter:
run: fp_filter.cwl
in:
reference: reference
bam: bam
vcf: bgzip_and_index/indexed_vcf
variant_caller:
valueFrom: "varscan"
sample_name: sample_name
min_var_freq: min_var_freq
out:
[unfiltered_vcf, filtered_vcf]