/
germline_wgs_gvcf.cwl
195 lines (194 loc) · 6.63 KB
/
germline_wgs_gvcf.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
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "wgs alignment and germline variant detection"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- $import: ../types/trimming_options.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "sequence: sequencing data and readgroup information"
doc: |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying
readgroup information. Note that in the @RG field ID and SM are required.
trimming:
type:
- ../types/trimming_options.yml#trimming_options
- "null"
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
emit_reference_confidence:
type:
type: enum
symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
ploidy:
type: int?
qc_intervals:
type: File
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
bqsr_known_sites:
type: File[]
secondaryFiles: [.tbi]
doc: "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis."
bqsr_intervals:
type: string[]?
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:
cram:
type: File
outputSource: index_cram/indexed_cram
mark_duplicates_metrics:
type: File
outputSource: alignment_and_qc/mark_duplicates_metrics
insert_size_metrics:
type: File
outputSource: alignment_and_qc/insert_size_metrics
insert_size_histogram:
type: File
outputSource: alignment_and_qc/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: alignment_and_qc/alignment_summary_metrics
gc_bias_metrics:
type: File
outputSource: alignment_and_qc/gc_bias_metrics
gc_bias_metrics_chart:
type: File
outputSource: alignment_and_qc/gc_bias_metrics_chart
gc_bias_metrics_summary:
type: File
outputSource: alignment_and_qc/gc_bias_metrics_summary
wgs_metrics:
type: File
outputSource: alignment_and_qc/wgs_metrics
flagstats:
type: File
outputSource: alignment_and_qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: alignment_and_qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: alignment_and_qc/verify_bam_id_depth
per_base_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: alignment_and_qc/summary_hs_metrics
gvcf:
type: File[]
outputSource: generate_gvcfs/gvcf
steps:
alignment_and_qc:
run: alignment_wgs.cwl
in:
reference: reference
sequence: sequence
trimming: trimming
bqsr_known_sites: bqsr_known_sites
omni_vcf: omni_vcf
intervals: qc_intervals
picard_metric_accumulation_level: picard_metric_accumulation_level
bqsr_intervals: bqsr_intervals
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
out:
[bam, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, alignment_summary_metrics, gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary, wgs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics]
extract_freemix:
in:
verify_bam_id_metrics: alignment_and_qc/verify_bam_id_metrics
out:
[freemix_score]
run:
class: ExpressionTool
requirements:
- class: InlineJavascriptRequirement
inputs:
verify_bam_id_metrics:
type: File
inputBinding:
loadContents: true
outputs:
freemix_score:
type: string?
expression: |
${
var metrics = inputs.verify_bam_id_metrics.contents.split("\n");
if ( metrics[0].split("\t")[6] == 'FREEMIX' ) {
return {'freemix_score': metrics[1].split("\t")[6]};
} else {
return {'freemix_score:': null };
}
}
generate_gvcfs:
run: ../subworkflows/gatk_haplotypecaller_iterator.cwl
in:
bam: alignment_and_qc/bam
reference: reference
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
contamination_fraction: extract_freemix/freemix_score
ploidy: ploidy
out:
[gvcf]
bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: alignment_and_qc/bam
reference: reference
out:
[cram]
index_cram:
run: ../tools/index_cram.cwl
in:
cram: bam_to_cram/cram
out:
[indexed_cram]