-
Notifications
You must be signed in to change notification settings - Fork 58
/
qc_wgs.cwl
145 lines (144 loc) · 4.57 KB
/
qc_wgs.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
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "WGS QC workflow"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: SubworkflowFeatureRequirement
inputs:
sample_name:
type: string?
default: 'final'
bam:
type: File
secondaryFiles: [^.bai]
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
intervals:
type: File
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
default: ALL_READS
minimum_mapping_quality:
type: int?
minimum_base_quality:
type: int?
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
outputs:
insert_size_metrics:
type: File
outputSource: collect_insert_size_metrics/insert_size_metrics
insert_size_histogram:
type: File
outputSource: collect_insert_size_metrics/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: collect_alignment_summary_metrics/alignment_summary_metrics
gc_bias_metrics:
type: File
outputSource: collect_gc_bias_metrics/gc_bias_metrics
gc_bias_metrics_chart:
type: File
outputSource: collect_gc_bias_metrics/gc_bias_metrics_chart
gc_bias_metrics_summary:
type: File
outputSource: collect_gc_bias_metrics/gc_bias_metrics_summary
wgs_metrics:
type: File
outputSource: collect_wgs_metrics/wgs_metrics
flagstats:
type: File
outputSource: samtools_flagstat/flagstats
verify_bam_id_metrics:
type: File
outputSource: verify_bam_id/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: verify_bam_id/verify_bam_id_depth
per_base_coverage_metrics:
type: File[]
outputSource: collect_hs_metrics/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: collect_hs_metrics/per_base_hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: collect_hs_metrics/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: collect_hs_metrics/per_target_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: collect_hs_metrics/summary_hs_metrics
steps:
collect_insert_size_metrics:
run: ../tools/collect_insert_size_metrics.cwl
in:
bam: bam
reference: reference
metric_accumulation_level: picard_metric_accumulation_level
out:
[insert_size_metrics, insert_size_histogram]
collect_alignment_summary_metrics:
run: ../tools/collect_alignment_summary_metrics.cwl
in:
bam: bam
reference: reference
metric_accumulation_level: picard_metric_accumulation_level
out:
[alignment_summary_metrics]
collect_gc_bias_metrics:
run: ../tools/collect_gc_bias_metrics.cwl
in:
sample_name: sample_name
bam: bam
reference: reference
metric_accumulation_level: picard_metric_accumulation_level
out:
[gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary]
collect_wgs_metrics:
run: ../tools/collect_wgs_metrics.cwl
in:
sample_name: sample_name
bam: bam
reference: reference
intervals: intervals
out:
[wgs_metrics]
samtools_flagstat:
run: ../tools/samtools_flagstat.cwl
in:
bam: bam
out: [flagstats]
verify_bam_id:
run: ../tools/verify_bam_id.cwl
in:
bam: bam
vcf: omni_vcf
out:
[verify_bam_id_metrics, verify_bam_id_depth]
collect_hs_metrics:
run: hs_metrics.cwl
in:
bam: bam
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
reference: reference
summary_intervals: summary_intervals
out:
[per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics]