nextflow.config

cleanup = false
workDir = '/pasteur/appa/scratch/jfumey/busco/work/'
env.OPENBLAS_NUM_THREADS=1
env.OMP_NUM_THREADS=1

executor {
    name = 'slurm'
    queueSize = 2000
}

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

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

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

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

singularity {
        enabled = true
        autoMounts = true
        runOptions = '--home $HOME:/home/$USER --bind /pasteur'
    cacheDir = '/pasteur/appa/scratch/jfumey/singularity'
}

process {
    executor='slurm'
    scratch=false
    maxRetries=30
    errorStrategy='retry'
	//queue='dedicated'
	//clusterOptions='--account=hubbioit --partition=hubbioit --qos=hubbioit'

    withLabel: ncbi{
        container="ncbi/edirect"
        executor='local'
    }

    withLabel: busco{
        container="ezlabgva/busco:v5.4.3_cv1"
        cpus=40
        memory='400G'
	//env.OPENBLAS_NUM_THREADS=1
	//env.OMP_NUM_THREADS=1
    }

    withLabel: selectGenome{
        container="evolbioinfo/python-evol:v3.8.2b"
        cpus=1
        memory='1G'
    }

    withLabel: dl{
        executor='local'
        errorStrategy='ignore'
    }

    withLabel: samtools{
        container='evolbioinfo/samtools:v1.11'
        cpus=1
        memory='10G'
    }

    withLabel: extractResults{
        container="evolbioinfo/python-evol:v3.8.2b"
        cpus=1
        memory='1G'
    }
}