-
Notifications
You must be signed in to change notification settings - Fork 6
/
maf2vcf_gz_workflow.cwl
63 lines (56 loc) · 1.08 KB
/
maf2vcf_gz_workflow.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
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
doc: "
Workflow to convert a maf file into a vcf.gz with .tbi index
"
requirements:
MultipleInputFeatureRequirement: {}
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
InlineJavascriptRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
maf_file: File
ref_fasta:
type: File
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
- .fai
- ^.dict
steps:
maf2vcf:
run: maf2vcf.cwl
in:
maf_file: maf_file
ref_fasta: ref_fasta
out:
[ output_file ]
sort_vcf:
run: vcf_sort.cwl
in:
vcf_file: maf2vcf/output_file
out:
[ output_file ]
zip_vcf:
run: bgzip.cwl
in:
input_file: sort_vcf/output_file
output_filename:
valueFrom: ${ return "variants.vcf.gz"; }
out:
[ output_file ]
index_vcf:
run: index_vcf.cwl
in:
input_file: zip_vcf/output_file
out:
[ indexed_file ]
outputs:
output_file:
type: File
outputSource: index_vcf/indexed_file