-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathrunCortexVarLowCoverage.nf
184 lines (120 loc) · 3.26 KB
/
runCortexVarLowCoverage.nf
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
#!/usr/bin/env nextflow
nextflowFolder = params.cloneDir + "/nextflow_scripts"
process preflightCheck {
output:
stdout into preflightStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/preflightCheck.nf
"""
}
if (params.runMakeSampleGraph == "y") {
process makeSampleDBGraph {
input:
val preflightFlag from preflightStdout
output:
stdout into makeSampleDBGraphStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/makeSampleGraph.nf
"""
}
} else {
makeSampleDBGraphStdout = Channel.from('DummyFlag')
}
if (params.runMakePoolAndCleanError == "y") {
process poolAndCleanErrors {
input:
val preflightFlag from preflightStdout
val makeSampleDBGraphFlag from makeSampleDBGraphStdout
output:
stdout into poolAndCleanErrorStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/poolAndCleanErrors.nf
"""
}
} else {
poolAndCleanErrorStdout = Channel.from('DummyFlag')
}
if (params.runCleanSampleGraph == "y") {
process cleanGraphPerSample {
input:
val preflightFlag from preflightStdout
val poolCleanStdout from poolAndCleanErrorStdout
output:
stdout into cleanGraphPerSampleStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/cleanGraphPerSampleLowCoverage.nf
"""
}
} else {
cleanGraphPerSampleStdout = Channel.from('DummyFlag')
}
if (params.runMakeReferenceGraph == "y") {
process makeReferenceGraph {
input:
val preflightFlag from preflightStdout
output:
stdout into makeReferenceGraphStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/makeReferenceGraph.nf
"""
}
} else {
makeReferenceGraphStdout = Channel.from('DummyFlag')
}
if (params.runMakeCombinationGraph == "y") {
process makeCombinationGraph {
input:
val preflightFlag from preflightStdout
val cleanGraphPerSampleFlag from cleanGraphPerSampleStdout
val makeRefGraphFlag from makeReferenceGraphStdout
output:
stdout into makeCombinationGraphStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/makeCombinationGraphLowCoverage.nf
"""
}
} else {
makeCombinationGraphStdout = Channel.from('DummyFlag')
}
if (params.runVariantCalling == "y") {
process variantCalling {
input:
val preflightFlag from preflightStdout
val makeCombinationGraphFlag from makeCombinationGraphStdout
output:
stdout into runVariantCallingStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/variantCalling.nf
"""
}
} else {
runVariantCallingStdout = Channel.from('DummyFlag')
}
if (params.runConversionToVCF == "y") {
process convertToVCF {
input:
val preflightFlag from preflightStdout
val variantCallingFlag from runVariantCallingStdout
script:
"""
cd ${params.resultsDir}
${params.nextflowDir} run ${nextflowFolder}/convertToVCF.nf
"""
}
} else {
runConversionToVCFStdout = Channel.from('DummyFlag')
}