nf-core/configs: Alliance Canada Configuration
Configuration for running nextflow on the clusters of the Digital Research Alliance of Canada. Invoke by specifying -profile alliance_canada.
You also need to supply the name of the group under which you are working or whose resource allocation you want to use by running export SLURM_ACCOUNT=<def-user> before you run any nf-core pipeline. If you run nf-core frequently and always use the same resource allocation, you may find it more convenient to add the SLURM_ACCOUNT environment variable to your ~/.bashrc file.
For detailed information on running nf-core pipelines on Alliance clusters, please visit the documentation: https://docs.alliancecan.ca/wiki/Nextflow
If you run into issues, please contact Alliance Support: https://docs.alliancecan.ca/wiki/Technical_support
Config file
params {
config_profile_description = 'Alliance Canada HPC config'
config_profile_contact = 'Jerry Li (@jerryakii)'
config_profile_url = 'https://docs.alliancecan.ca/wiki/Nextflow'
max_time = 168.h
max_cpus = 64
max_memory = 240.GB
}
cleanup = true
singularity {
enabled = true
autoMounts = true
}
apptainer {
autoMounts = true }
// Group name for resource allocation must be supplied as environment variable
process {
executor = 'slurm'
clusterOptions = "--account=${System.getenv('SLURM_ACCOUNT')}"
maxRetries = 1
errorStrategy = { task.exitStatus in [125,139] ? 'retry' : 'finish' }
cpu = 1
time = '3h'
resourceLimits = [
memory: 240.GB,
cpus: 64,
time: 168.h
]
}
executor {
pollInterval = '60 sec'
submitRateLimit = '60/1min'
queueSize = 100
}
// Cluster name is available as environment variable
// If not found, default to narval as it has the lowest limits
hostname = "narval"
try {
hostname = "${System.getenv('HOSTNAME')}"
} catch (java.io.IOException e) {
System.err.println("WARNING: Could not determine current cluster, defaulting to narval")
}
// Cluster Narval
if (hostname.startsWith("narval")) {
params.config_profile_description = 'Alliance Canada (Narval) cluster profile provided by nf-core/configs.'
params.max_memory = 249.GB
params.max_cpus = 64
process {
resourceLimits = [
memory: 249.GB,
cpus: 64,
time: 168.h
]
}
}
// Cluster Rorqual
if (hostname.startsWith("rorqual")) {
params.config_profile_description = 'Alliance Canada (Rorqual) cluster profile provided by nf-core/configs.'
params.max_memory = 750.GB
params.max_cpus = 192
process {
resourceLimits = [
memory: 750.GB,
cpus: 192,
time: 168.h
]
}
}
// Cluster Trillium
if (hostname.startsWith("tri")) {
params.config_profile_description = 'Alliance Canada (Trillium) cluster profile provided by nf-core/configs.'
params.max_memory = null
params.max_cpus = null
process {
clusterOptions = "--account=${System.getenv('SLURM_ACCOUNT')} --nodes=1"
resourceLimits = [
time: 168.h
]
}
executor {
queueSize = 500
}
}
// Cluster Nibi
if (hostname.contains("nibi")) {
params.config_profile_description = 'Alliance Canada (Nibi) cluster profile provided by nf-core/configs.'
params.max_memory = 750.GB
params.max_cpus = 192
process {
resourceLimits = [
memory: 750.GB,
cpus: 192,
time: 168.h
]
}
}
// Cluster Fir
// not sure what the hostname is so set it as a profile
profiles {
fir {
params.config_profile_description = 'Alliance Canada (Fir) cluster profile provided by nf-core/configs.'
params.max_memory = 750.GB
params.max_cpus = 192
process {
resourceLimits = [
memory: 750.GB,
cpus: 192,
time: 168.h
]
}
}
}
executor
contact
