nextflow.config

includeConfig "${baseDir}/parameters/process/general_params.config"
includeConfig "${baseDir}/parameters/process/globalfilt_params.config"
includeConfig "${baseDir}/parameters/process/genstruct_params.config"
includeConfig "${baseDir}/parameters/process/treemix.config"
includeConfig "${baseDir}/parameters/process/sig_sel_params.config"


profiles{
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    mamba {
        conda.enabled          = true
        conda.useMamba         = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    arm {
        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
	singularity.runOptions = '-B $SINGULARITY_TMPDIR'
	singularity.envWhitelist = ['SINGULARITY_TMPDIR']
    }
    podman {
        podman.enabled         = true
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    shifter {
        shifter.enabled        = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    gitpod {
        executor.name          = 'local'
        executor.cpus          = 16
        executor.memory        = 60.GB
    }
    test_genstruct { includeConfig 'parameters/test/test_genetic_structure.config'      }
    test_filt { includeConfig 'parameters/test/globalfilt_params.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}

process{
        executor="local"
	time = "48h"
        //queue = "serial_std"
        withLabel: 'twoCpus' {
            memory='1G'
            cpus='2'
            //time='48h'
        }
        withLabel: 'oneCpu' {
            //queue = "bigcpus"
            memory='1G'
            cpus='1'
            //time='48h'
        }
        withLabel: 'sixteenCpus' {
            memory='24G'
            cpus='10'
            //time='48h'
        }
        withLabel: 'fourCpus' {
            memory='6G'
            cpus='4'
            //time='48h'
        }
}