43 lines
1 KiB
Text
43 lines
1 KiB
Text
params {
|
|
reference = null
|
|
|
|
// Config options
|
|
config_profile_name = null
|
|
config_profile_description = null
|
|
custom_config_version = 'master'
|
|
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
|
|
config_profile_contact = null
|
|
config_profile_url = null
|
|
|
|
// Max resource options
|
|
// Defaults only, expecting to be overwritten
|
|
max_memory = '128.GB'
|
|
max_cpus = 16
|
|
max_time = '240.h'
|
|
}
|
|
|
|
process {
|
|
errorStrategy = 'finish'
|
|
time = '7d'
|
|
|
|
withName: 'HAPLINK_ML_HAPLOTYPES' {
|
|
ext.ml_args = """
|
|
--simulated-reads \\
|
|
--overlap-min 20 \\
|
|
--overlap-max 8000 \\
|
|
"""
|
|
}
|
|
}
|
|
|
|
try {
|
|
includeConfig "${params.custom_config_base}/nfcore_custom.config"
|
|
} catch (Exception e) {
|
|
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
|
|
}
|
|
|
|
singularity.enabled = true
|
|
|
|
env {
|
|
R_PROFILE_USER = "/.Rprofile"
|
|
R_ENVIRON_USER = "/.Renviron"
|
|
}
|