-
Notifications
You must be signed in to change notification settings - Fork 2
/
exomeseq-gatk4-03-organizedirectories.cwl
80 lines (78 loc) · 1.85 KB
/
exomeseq-gatk4-03-organizedirectories.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
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
fastp_html_reports: File[]
fastp_json_reports: File[]
bams_markduplicates: File[]
metrics_markduplicates: File[]
raw_variants: File[]
bams_recalibrated: File[]
outputs:
fastp_html_reports_dir:
type: Directory
outputSource: org_fastp_html_reports/outdir
fastp_json_reports_dir:
type: Directory
outputSource: org_fastp_json_reports/outdir
bams_markduplicates_dir:
type: Directory
outputSource: org_bams_markduplicates/outdir
metrics_markduplicates_dir:
type: Directory
outputSource: org_metrics_markduplicates/outdir
raw_variants_dir:
type: Directory
outputSource: org_raw_variants/outdir
bams_recalibrated_dir:
type: Directory
outputSource: org_bams_recalibrated/outdir
steps:
org_fastp_html_reports:
run: ../utils/files-to-directory.cwl
in:
name:
default: 'fastp-html-reports'
files: fastp_html_reports
out:
- outdir
org_fastp_json_reports:
run: ../utils/files-to-directory.cwl
in:
name:
default: 'fastp-json-reports'
files: fastp_json_reports
out:
- outdir
org_bams_markduplicates:
run: ../utils/files-to-directory.cwl
in:
name:
default: 'bams-markduplicates'
files: bams_markduplicates
out:
- outdir
org_metrics_markduplicates:
run: ../utils/files-to-directory.cwl
in:
name:
default: 'metrics-markduplicates'
files: metrics_markduplicates
out:
- outdir
org_raw_variants:
run: ../utils/files-to-directory.cwl
in:
name:
default: 'gvcfs'
files: raw_variants
out:
- outdir
org_bams_recalibrated:
run: ../utils/files-to-directory.cwl
in:
name:
default: 'bams-recalibrated'
files: bams_recalibrated
out:
- outdir