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|
params.worker = 1
manifest {
homePage = 'https://github.com/gem-pasteur/macsyfinder'
description = 'Workflow to run MacSyFinder on large dataset.'
mainScript = 'parallel_macsyfinder.nf'
defaultBranch = 'master'
nextflowVersion = '>=0.31'
}
profiles {
standard {
executor {
name = 'local'
queueSize = 4
}
process {
errorStrategy = 'terminate'
withName: macsyfinder {
cpus = params.worker
}
}
}
standard_apptainer {
executor {
name = 'local'
queueSize = 4
}
process {
errorStrategy = 'terminate'
container = '/path/to/macsyfinder/Apptainer/macsyfinder-2.1rc1.simg'
withName: macsyfinder
cpus = params.worker
}
}
singularity {
enabled = true
}
}
standard_docker {
executor {
name = 'local'
queueSize = 4
}
process {
errorStrategy = 'terminate'
container = 'macsyfinder'
withName: macsyfinder {
cpus = params.worker
}
}
docker {
enabled = true
runOptions = '--user $(id -u):$(id -g)'
}
}
cluster {
executor {
name = 'slurm'
queueSize = 500
}
process {
errorStrategy = 'retry'
maxRetries = 50
queue = 'common,dedicated'
clusterOptions = '--qos=fast'
withName: macsyfinder {
cpus = params.worker
}
}
}
cluster_apptainer {
executor {
name = 'slurm'
queueSize = 500
}
process {
errorStrategy = 'retry'
maxRetries = 100
container = '/path/to/macsyfinder-apptainer-image'
queue = 'common,dedicated'
clusterOptions = '--qos=fast'
withName: macsyfinder {
cpus = params.worker
}
withName: split {
memory = 20.GB
}
}
singularity {
enabled = true
runOptions = '-H $HOME -B /pasteur'
autoMounts = false
}
}
}
|
