-
Notifications
You must be signed in to change notification settings - Fork 9
/
nextflow.config.v0.8
142 lines (132 loc) · 5.09 KB
/
nextflow.config.v0.8
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
// Singularity containter cache. Change this as appropriate
singularity {
cacheDir = "/opt/singularity_cache"
}
// Process settings. Set job scheduler if appropriate (SLURM, PBS e.g.)
// If your job scheduler has different queues/partitions for cpu and gpu, please also set them here
process {
executor = params.executor
withLabel: cpu { queue = 'main' }
withLabel: gpu { queue = 'gpu' }
}
// Default parameters. Commandline parameters will take priority over these
params {
executor = "local"
outdir = './results'
basecalling = false
demultiplexing = false
gpu = true
fast5 = false
fastq = false
datadir = false
demultiplexer = 'guppy'
//Path to the Guppy GPU and CPU binary folder (v3.4.3). Change this as appropriate when providing Guppy as a binary folder and do not forget the "/" at the end of the path
guppy_gpu_folder = "/scratch/ont-guppy/bin/"
guppy_cpu_folder = "/scratch/ont-guppy-cpu/bin/"
//Uncomment the two following lines when providing Guppy container images (and comment the two previous lines)
//guppy_gpu_folder = ""
//guppy_cpu_folder = ""
guppy_config_gpu = "dna_r9.4.1_450bps_hac.cfg"
guppy_config_cpu = "dna_r9.4.1_450bps_fast.cfg"
kit = false
flowcell = false
guppy_gpu_device = "auto"
guppy_num_callers = 8
guppy_cpu_threads_per_caller = 1
guppy_basecaller_args = "--recursive --trim_barcodes -q 0"
guppy_barcoder_args = "--recursive --trim_barcodes -q 0"
guppy_barcode_kits= "SQK-RBK004"
guppy_barcoder_threads = 2
qcat_args = ""
skip_pycoqc = false
skip_rasusa = true
skip_porechop = false
skip_filtering = false
rasusa_coverage = 100
filtering = "japsa"
porechop_args = ""
porechop_threads = 4
japsa_args = "--lenMin 1000 --qualMin 10"
filtlong_args = "--min_length 1000 --keep_percent 90"
flye_args = "--plasmids"
flye_threads = 4
polisher = "medaka"
racon_nb = 4
racon_args = "-m 8 -x -6 -g -8 -w 500"
racon_threads = 4
medaka_model = "r941_min_high"
medaka_threads = 8
nextpolish_threads = 4
nextpolish_task_SR = "1212"
nextpolish_task_LR = "55"
skip_illumina = false
fixstart_args = ""
skip_fixstart = false
quast_threads = 1
quast_args = ""
skip_quast = false
}
// Debug and report options
trace {
enabled = true
file = "${params.outdir}/trace.txt"
}
timeline {
enabled = true
file = "${params.outdir}/timeline.html"
}
report {
enabled = true
file = "${params.outdir}/report.html"
}
dag {
enabled = true
file = "${params.outdir}/flowchart_dag.svg"
}
// Not generally user-modifiable !!!
process {
withLabel: big_mem { memory = 32.GB }
//Path to the Guppy GPU and CPU container images (v3.4.3). Uncomment and change this as appropriate if providing Guppy as a container image.
//withLabel: guppy_gpu { container = '' }
//withLabel: guppy_cpu { container = '' }
withLabel: pycoqc { container = 'docker://quay.io/biocontainers/pycoqc:2.5.0.23--py_0' }
withName: demultiplexing_qcat { container = 'docker://quay.io/biocontainers/qcat:1.0.1--py_0' }
withName: rasusa { container = 'docker://quay.io/biocontainers/rasusa:0.3.0--h516909a_0' }
withName: porechop { container = 'docker://quay.io/biocontainers/porechop:0.2.3_seqan2.1.1--0' }
withName: filtlong { container = 'docker://quay.io/biocontainers/filtlong:0.2.0--he513fc3_3' }
withName: japsa { container = 'docker://vmurigneux/japsa:latest' }
withName: flye { container = 'docker://quay.io/biocontainers/flye:2.5--py27he513fc3_0' }
withName: racon_cpu { container = 'docker://vmurigneux/racon:1.4.9' }
withLabel: medaka { container = 'docker://quay.io/biocontainers/medaka:0.10.0--py36hbcae180_1' }
withLabel: nextpolish { container = 'docker://pvstodghill/nextpolish:1.1.0__2020-05-12' }
withLabel: circlator { container = 'docker://quay.io/biocontainers/circlator:1.5.5--py_3' }
withName: quast { container = 'docker://quay.io/biocontainers/quast:5.0.2--py37pl526hb5aa323_2' }
errorStrategy = 'ignore'
}
mounts {
fast5 = ""
fastq = ""
datadir = ""
if (params.fast5 != false) {
fast5 = "-B \"`[[ \"${params.fast5}\" =~ ^/ ]] && echo ${params.fast5} || echo ${PWD}/${params.fast5}`\""
}
if (params.fastq != false){
fastq = "-B \"`[[ \"${params.fastq}\" =~ ^/ ]] && echo ${params.fastq} || echo ${PWD}/${params.fastq}`\""
}
if (params.datadir != false){
datadir = "-B \"`[[ \"${params.datadir}\" =~ ^/ ]] && echo ${params.datadir} || echo ${PWD}/${params.datadir}`\""
}
}
singularity {
enabled = true
autoMounts = false
runOptions = "-B \"$launchDir\" $mounts.fast5 $mounts.fastq $mounts.datadir -B \"`[[ \"${params.outdir}\" =~ ^/ ]] && echo ${params.outdir} || echo ${PWD}/${params.outdir}`\""
}
manifest {
name = 'microPIPE'
author = 'Valentine Murigneux'
description = 'Bacterial genome assembly pipeline'
homePage = 'https://github.com/BeatsonLab-MicrobialGenomics/micropipe'
mainScript = 'main.nf'
version = '0.8'
}