-
Notifications
You must be signed in to change notification settings - Fork 2
/
nextflow.config
125 lines (110 loc) · 3.6 KB
/
nextflow.config
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
params {
// Genotype QC parameters (GRCh38)
ref_genome = "genimpute_complete_reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa"
ref_panel = "genimpute_complete_reference/1KG_30x-GRCh38_variant_information_with_X"
// Impututation parameters
eagle_genetic_map = "genimpute_complete_reference/genetic_map_hg38_withX.txt.gz"
eagle_phasing_reference = "genimpute_complete_reference/Eagle_1KG_30x-GRCh38_phasing_reference/"
// Minimac4 parameters
minimac_imputation_reference = "genimpute_complete_reference/Minimac_1KG_30x-GRCh38_imputation_reference/"
// CrossMap.py parameters
chain_file = "data/GRCh37_to_GRCh38.chain"
r2_thresh = 0.4
skip_crossmap = false
// Chromosome annotation parameters (used during plink_to_vcf())
annotation_file_23_to_X = "data/chr23_to_X.txt"
// X chromosome imputation
impute_PAR = false
impute_non_PAR = false
outdir = './results'
custom_config_version = 'master'
tracedir = "${params.outdir}/pipeline_info"
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 16
max_time = 240.h
}
//Define Docker/Singularity container
process.container = 'quay.io/eqtlcatalogue/genimpute:v20.06.1'
//Overwrite trace and report files when resuming
trace.overwrite = true
report.overwrite = true
timeline.overwrite = true
includeConfig 'conf/base.config'
includeConfig "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/nfcore_custom.config"
profiles {
tartu_hpc { includeConfig 'conf/tartu_hpc.config'}
eqtl_catalogue {
includeConfig 'conf/tartu_hpc.config'
includeConfig 'conf/eqtl_catalogue.config'
}
awsbatch { includeConfig 'conf/awsbatch.config' }
conda { process.conda = "$baseDir/environment.yml" }
debug { process.beforeScript = 'echo $HOSTNAME' }
docker {
docker.enabled = true
}
singularity {
singularity.enabled = true
}
test { includeConfig 'genotype_qc/conf/test.config' }
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
timeline {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_timeline.html"
}
report {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_report.html"
}
trace {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_trace.txt"
}
dag {
enabled = true
file = "${params.tracedir}/nf-core/qtlmap_dag.svg"
}
manifest {
name = 'eQTL-Catalogue/genimpute'
author = 'Kaur Alasoo'
homePage = 'https://github.com/eQTL-Catalogue/genimpute'
description = ' '
mainScript = 'main.nf'
nextflowVersion = '>=19.10.0'
version = '1.0dev'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if(type == 'memory'){
try {
if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'time'){
try {
if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'cpus'){
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}