/
SuperMiniTyper_Pipeline1_GPU.wdl
78 lines (60 loc) · 1.49 KB
/
SuperMiniTyper_Pipeline1_GPU.wdl
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
task Pipeline1_GPU_cudamapper {
File inputFASTQ
Int diskGB = 32
Int threads = 8
Int kmerSize = 15
Int windowSize = 15
Int indexSize = 10000
Int targetIndexSize = 10000
Int dropLengthLower = 10000
String outbase = basename(inputFASTQ)
command {
cudamapper -k ${kmerSize} -w ${windowSize} -i ${indexSize} -t ${targetIndexSize} ${inputFASTQ} ${inputFASTQ} | fpa drop -l ${dropLengthLower} > ${outbase}.paf
}
runtime {
docker: "ncbicodeathons/superminityper:0.1"
cpu : "${threads}"
memory : "16 GB"
disk : "local-disk " + diskGB + " HDD"
preemptible : 4
}
output {
File outputPAF = "${outbase}.paf"
}
}
task Pipeline1_GPU_seqwish {
File inputFASTQ
File inputPAF
Int diskGB = 32
Int threads = 8
String outbase = basename(inputFASTQ)
command {
seqwish -s ${inputFASTQ} -p ${inputPAF} -b ${outbase}.graph -g ${outbase}.gfa -t ${threads}
}
runtime {
docker: "ncbicodeathons/superminityper:0.1-cpu"
cpu : "${threads}"
memory : "16 GB"
disk : "local-disk " + diskGB + " HDD"
preemptible : 4
}
output {
File outputGFA = "${outbase}.gfa"
File outputGRAPH = "${outbase}.graph"
}
}
workflow SuperMiniTyper_Pipeline1_GPU {
File inputFASTQ
Int diskGB = 32
Int threads = 8
call Pipeline1_GPU_cudamapper {
input:
inputFASTQ=inputFASTQ,
diskGB=diskGB
}
call Pipeline1_GPU_seqwish {
input:
inputFASTQ=inputFASTQ,
inputPAF=Pipeline1_GPU_cudamapper.outputPAF
}
}