/
qc_exome.cwl
142 lines (141 loc) · 4.54 KB
/
qc_exome.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
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Exome QC workflow"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
secondaryFiles: [^.bai]
reference:
type: string
bait_intervals:
type: File
target_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
hs_metrics:
type: File
outputSource: collect_roi_hs_metrics/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: collect_detailed_hs_metrics/summary_hs_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
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_roi_hs_metrics:
run: ../tools/collect_hs_metrics.cwl
in:
bam: bam
reference: reference
metric_accumulation_level:
valueFrom: "ALL_READS"
bait_intervals: bait_intervals
target_intervals: target_intervals
per_target_coverage:
default: false
per_base_coverage:
default: false
output_prefix:
valueFrom: "roi"
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
out:
[hs_metrics]
collect_detailed_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]
samtools_flagstat:
run: ../tools/samtools_flagstat.cwl
in:
bam: bam
out: [flagstats]
select_variants:
run: ../tools/select_variants.cwl
in:
reference: reference
vcf: omni_vcf
interval_list: target_intervals
out:
[filtered_vcf]
verify_bam_id:
run: ../tools/verify_bam_id.cwl
in:
bam: bam
vcf: select_variants/filtered_vcf
out:
[verify_bam_id_metrics, verify_bam_id_depth]