-
Notifications
You must be signed in to change notification settings - Fork 3
/
bams2gvcf.woBQSR_female.cwl
186 lines (153 loc) · 5.16 KB
/
bams2gvcf.woBQSR_female.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
#!/usr/bin/env cwl-runner
class: Workflow
id: bam2gvcf-woBQSR-female
label: bam2gvcf-woBQSR-female
cwlVersion: v1.0
$namespaces:
edam: 'http://edamontology.org/'
requirements:
SubworkflowFeatureRequirement: {}
inputs:
reference:
type: File
format: edam:format_1929
doc: FastA file for reference genome
secondaryFiles:
- .fai
- ^.dict
reference_interval_name_autosome:
type: string
default: autosome
doc: interval name for reference genome (autosome)
reference_interval_list_autosome:
type: File
doc: interval list for reference genome (autosome)
reference_interval_name_chrX:
type: string
default: chrX
doc: interval name for reference genome (chrX)
reference_interval_list_chrX:
type: File
doc: interval list for reference genome (chrX)
reference_interval_name_chrY:
type: string
default: chrY
doc: interval name for reference genome (chrY)
reference_interval_list_chrY:
type: File
doc: interval list for reference genome (chrY)
bam_files:
type: File[]
format: edam:format_2572
doc: array of input BAM alignment files (each file should be sorted)
nthreads:
type: int
doc: number of cpu cores to be used
outprefix:
type: string
doc: Output prefix name
steps:
bams2gvcf_woBQSR:
label: bams2gvcf_woBQSR
doc: Call haplotypes from bam files
run: ../Workflows/bams2gvcf.woBQSR.cwl
in:
bam_files: bam_files
outprefix: outprefix
reference: reference
reference_interval_name_autosome: reference_interval_name_autosome
reference_interval_list_autosome: reference_interval_list_autosome
reference_interval_name_chrX: reference_interval_name_chrX
reference_interval_list_chrX: reference_interval_list_chrX
reference_interval_name_chrY: reference_interval_name_chrY
reference_interval_list_chrY: reference_interval_list_chrY
nthreads: nthreads
out:
- rmdup_bam
- rmdup_metrics
- rmdup_log
- picard_collect_multiple_metrics_alignment_summary_metrics
- picard_collect_multiple_metrics_insert_size_metrics
- picard_collect_multiple_metrics_log
- samtools_flagstat_flagstat
- samtools_idxstats_idxstats
- picard_CollectWgsMetrics_autosome_wgs_metrics
- picard_CollectWgsMetrics_autosome_log
- picard_CollectWgsMetrics_chrX_wgs_metrics
- picard_CollectWgsMetrics_chrX_log
- picard_CollectWgsMetrics_chrY_wgs_metrics
- picard_CollectWgsMetrics_chrY_log
- gatk3_HaplotypeCaller_vcf
- gatk3_HaplotypeCaller_log
outputs:
rmdup_bam:
type: File
format: edam:format_2572
outputSource: bams2gvcf_woBQSR/rmdup_bam
secondaryFiles:
- ^.bai
rmdup_metrics:
type: File
outputSource: bams2gvcf_woBQSR/rmdup_metrics
rmdup_log:
type: File
outputSource: bams2gvcf_woBQSR/rmdup_log
picard_collect_multiple_metrics_alignment_summary_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_alignment_summary_metrics
secondaryFiles:
- ^.bait_bias_detail_metrics
- ^.bait_bias_summary_metrics
- ^.base_distribution_by_cycle_metrics
- ^.base_distribution_by_cycle.pdf
- ^.error_summary_metrics
- ^.gc_bias.detail_metrics
- ^.gc_bias.pdf
- ^.gc_bias.summary_metrics
- ^.pre_adapter_detail_metrics
- ^.pre_adapter_summary_metrics
- ^.quality_by_cycle_metrics
- ^.quality_by_cycle.pdf
- ^.quality_distribution_metrics
- ^.quality_distribution.pdf
picard_collect_multiple_metrics_insert_size_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_insert_size_metrics
secondaryFiles:
- ^.insert_size_histogram.pdf
picard_collect_multiple_metrics_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_collect_multiple_metrics_log
samtools_flagstat_flagstat:
type: File
outputSource: bams2gvcf_woBQSR/samtools_flagstat_flagstat
samtools_idxstats_idxstats:
type: File
outputSource: bams2gvcf_woBQSR/samtools_idxstats_idxstats
picard_CollectWgsMetrics_autosome_wgs_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_autosome_wgs_metrics
picard_CollectWgsMetrics_autosome_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_autosome_log
picard_CollectWgsMetrics_chrX_wgs_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrX_wgs_metrics
picard_CollectWgsMetrics_chrX_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrX_log
picard_CollectWgsMetrics_chrY_wgs_metrics:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrY_wgs_metrics
picard_CollectWgsMetrics_chrY_log:
type: File
outputSource: bams2gvcf_woBQSR/picard_CollectWgsMetrics_chrY_log
gatk3_HaplotypeCaller_vcf:
type: File
format: edam:format_3016
outputSource: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_vcf
secondaryFiles:
- .tbi
gatk3_HaplotypeCaller_log:
type: File
outputSource: bams2gvcf_woBQSR/gatk3_HaplotypeCaller_log