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
|
#!/usr/bin/env nextflow
python3 = "python3"
resfinder = "/home/projects/cge/apps/resfinder/resfinder/run_resfinder.py"
params.indir = './'
params.ext = '.fq.gz'
params.outdir = '.'
params.species = 'other'
println("Search pattern: $params.indir*{1,2}$params.ext")
Channel
.fromFilePairs("$params.indir*{1,2}$params.ext", followLinks: true)
.set{ infile_ch }
process resfinder{
cpus 5
time '30m'
memory '1 GB'
clusterOptions '-V -W group_list=cge -A cge'
executor "PBS"
input:
set sampleID, file(datasetFile) from infile_ch
output:
stdout result
"""
set +u
module unload mgmapper metabat fastqc
module unload ncbi-blast perl
source /home/projects/cge/apps/env/rf4_env/bin/activate
module load perl
module load ncbi-blast/2.8.1+
if [ $params.species = 'other' ]
then
$python3 $resfinder -acq -ifq $datasetFile -o '$params.outdir/$sampleID' -s '$params.species'
else
$python3 $resfinder -acq -ifq $datasetFile -o '$params.outdir/$sampleID' -s '$params.species' --point
fi
"""
}
/*
result.subscribe {
println it
}
*/
|
