-
Notifications
You must be signed in to change notification settings - Fork 58
/
strelka_and_post_processing.cwl
83 lines (82 loc) · 2.01 KB
/
strelka_and_post_processing.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
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "strelka workflow"
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
tumor_bam:
type: File
secondaryFiles: [.bai,^.bai]
normal_bam:
type: File
secondaryFiles: [.bai,^.bai]
reference:
type: string
interval_list:
type: File
exome_mode:
type: boolean
cpu_reserved:
type: int?
default: 8
outputs:
unfiltered_vcf:
type: File
outputSource: filter/unfiltered_vcf
secondaryFiles: [.tbi]
filtered_vcf:
type: File
outputSource: filter/filtered_vcf
secondaryFiles: [.tbi]
steps:
strelka:
run: ../tools/strelka.cwl
in:
tumor_bam: tumor_bam
normal_bam: normal_bam
reference: reference
exome_mode: exome_mode
cpu_reserved: cpu_reserved
out:
[indels, snvs]
process:
scatter: vcf
run: strelka_process_vcf.cwl
in:
vcf: [strelka/snvs, strelka/indels]
out:
[processed_vcf]
merge:
run: ../tools/merge_vcf.cwl
in:
vcfs: process/processed_vcf
out:
[merged_vcf]
index_full:
run: ../tools/index_vcf.cwl
in:
vcf: merge/merged_vcf
out:
[indexed_vcf]
region_filter:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: index_full/indexed_vcf
interval_list: interval_list
out:
[filtered_vcf]
filter:
run: fp_filter.cwl
in:
reference: reference
bam: tumor_bam
vcf: region_filter/filtered_vcf
variant_caller:
valueFrom: "strelka"
out:
[unfiltered_vcf, filtered_vcf]