bayesian_bootstrap/nextflow.config at main · evolbioinfo/bayesian_bootstrap · GitHub

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// Preform work directory cleanup after a successful run
cleanup = true

executor {
    name = 'slurm'
    queueSize = 10000
}

report {
       enabled = true
       file = 'reports/report.html'
       overwrite=true
}

trace {
    enabled = true
    file = 'reports/trace.txt'
    overwrite=true
}

timeline {
    enabled = true
    file = 'reports/timeline.html'
    overwrite=true
}

dag {
    enabled = true
    file = 'reports/dag.dot'
    overwrite=true
}

profiles {
    standard {
        process {
            scratch=false
            maxRetries=30
            errorStrategy='retry'
	    cache='deep'

            withLabel: phyml {
                container='evolbioinfo/phyml:v3.3.20200621'
                cpus=1
                memory={3.GB * task.attempt}
            }

            withLabel: gotree {
                container='evolbioinfo/gotree:v0.4.2'
                cpus=1
                memory='15G'
            }

            withLabel: goalign {
                container='evolbioinfo/goalign:dev0537492'
                cpus=1
                memory='20G'
            }

            withLabel: r {
                container='evolbioinfo/r-extended:v4.3.3'
                cpus=1
                memory='20G'
            }
        }
    }
    local {
        process.executor = 'local'
    }
    pasteur {
        process.executor = 'slurm'
        process.queue = {task.attempt > 1  ? "cnrvir" : "common,dedicated" }
	clusterOptions = {task.attempt > 1  ? "-A cnrvir" : "--qos=fast" }
    }
    arm64 {
        process {
	    withLabel: phyml {
                container='evolbioinfo/phyml:v3.3.20200621_arm64'
                cpus=1
                memory={3.GB * task.attempt}
            }
	}
    }
    slurm {
        process.executor = 'slurm'
        process.queue = "queue"
	clusterOptions = "--qos=fast"
    }
    singularity {
       singularity.enabled = true
       singularity.autoMounts = true
       singularity.runOptions = "--no-home"
       singularity.cacheDir = "singularity"
    }
    docker {
       docker.enabled = true
       docker.runOptions = "--entrypoint ''"
    }
}

params {
    msa = "data/alignment.fasta"
    results="results"
    collapse=0.1
    collapseref=false
    nboot = 200
}