-
Notifications
You must be signed in to change notification settings - Fork 0
/
STAR-index.wdl
57 lines (42 loc) · 1.17 KB
/
STAR-index.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
workflow SRA_Downloads{
File genomefasta
File genomeGTF
Int readLength
File genomefastaIndex
call create_index {
input:
genomefasta = genomefasta,
genomeGTF = genomeGTF,
readLength = readLength,
genomefastaIndex = genomefastaIndex
}
}
task create_index {
File genomefasta
File genomeGTF
Int readLength
File genomefastaIndex
command <<<
# create index (prefix: 'index')
mkdir out && cd out
rsem-prepare-reference --gtf ${genomeGTF} -p 16 --star --gtf ${genomeGTF} ${genomefasta} index --star-sjdboverhang ${readLength}
STAR --runMode genomeGenerate \
--runThreadN 16 \
--genomeFastaFiles ${genomefasta} \
--sjdbGTFfile ${genomeGTF} \
--sjdbOverhang ${readLength} \
--outFileNamePrefix index
la -lah
cd .. && tar -cvzf out.tar.gz out
>>>
output {
File rsem_index = "out.tar.gz"
}
runtime {
disks: "local-disk 125 HDD"
cpu: 16
memory: "60 GB"
docker: "gargk/sra"
preemptible: 3
}
}