nextflow.config

includeConfig 'external-modules/spark/nextflow.config'

manifest {
    name = 'expansion-microscopy-pipeline'
    author = 'Janelia Scientific Computing Software'
    homePage = 'https://github.com/JaneliaSciComp/expansion-microscopy-pipeline'
    description = 'Analysis pipelines for Expansion Microscopy'
    nextflowVersion = '>=20.10.0'
    version = '1.0.0'
}

params {
    lsf_opts = ''
    runtime_opts = ''
    singularity_cache_dir = "$HOME/.singularity_cache"
    vmf = '-B' // volume mounting flag
}

profiles {

    standard {
        docker.enabled = false
        singularity.enabled = true
    }

    lsf {
        process {
            executor = 'lsf'
            beforeScript = 'echo "Host: $HOSTNAME"' 
            clusterOptions = params.lsf_opts

            withLabel: withGPU {
                queue = 'gpu_rtx'
                clusterOptions = '-gpu "num=1" ' + params.lsf_opts
            }

            withLabel: withAVX2 {
                clusterOptions = '-R"select[avx2]" ' + params.lsf_opts
            }

            withLabel: preferLocal {
                executor = 'local'
            }
        }
        docker.enabled = false
        singularity.enabled = true
    }

    localdocker {
        docker.enabled = true
        singularity.enabled = false
        params.vmf = '-v'
    }
}

singularity {
    autoMounts = true
    cacheDir = "${params.singularity_cache_dir}"
    runOptions = "--nv -e --env USER=$USER ${params.runtime_opts}"
}