params {
    gene = "nat2"
}


process {

    // ALL PROCESSES
    cache = true
    stageInMode = 'symlink'
    stageOutMode = 'rsync'
   // scratch = "$HOME/tmp"  // clean this regularly

    // Containers

    // Singularity

//    withLabel: phase {
//    singularity.enabled	= false
    //container = "$PWD/containers/whatshap.sif" // this can be generated from docker://pacificbiosciences/whatshap
//    }

    withName: call_snvs1 {
    singularity.enabled = true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: call_snvs2 {
    singularity.enabled	= true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: call_sv_del {
    singularity.enabled	= true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: call_sv_dup {
    singularity.enabled	= true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: get_depth {
    singularity.enabled	= true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: format_snvs {
    singularity.enabled	= true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: get_core_var {
    singularity.enabled	= true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: analyse_1 {
    singularity.enabled = true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: analyse_2 {
    singularity.enabled = true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: analyse_3 {
    singularity.enabled = true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: analyse_4 {
    singularity.enabled = true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    withName: call_stars {
    singularity.enabled = true
    container = "$PWD/containers/stellarpgx-dev.sif"
    }

    
    // Docker
    // container = "twesigomwedavid/stellarpgx-dev:latest" // Note that this Docker build needs to be pulled from Do

}