def fs = File.separator
def pd = "${projectDir}"

// Global parameters
includeConfig "${pd}${fs}conf${fs}manifest.config"
includeConfig "${pd}${fs}conf${fs}base.config"

// Include FASTQ config to prepare for a case when the entry point is 
// FASTQ metadata CSV or FASTQ input directory
includeConfig "${pd}${fs}conf${fs}fastq.config"

if (params.pipeline != null) {
    try {
        includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
    } catch (Exception e) {
        System.err.println('-'.multiply(params.linewidth) + "\n" +
            "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
            '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
            "default pipeline configuration. Please provide a pipeline \n" +
            "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
        System.exit(1)
    }
}

// Include modules' config last.
includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
includeConfig "${pd}${fs}conf${fs}modules.config"

// Nextflow runtime profiles
conda.cacheDir = '/tmp'
singularity.cacheDir = '/tmp'

// Cleanup after running
cleanup = true

profiles {
    standard {
        process.executor = 'local'
        process.cpus = 1
        params.enable_conda = false
        params.enable_module = true
        singularity.enabled = false
        docker.enabled = false
    }

    stdkondagac {
        process.executor = 'local'
        process.cpus = 4
        params.enable_conda = true
        params.enable_module = false
        singularity.enabled = false
        docker.enabled = false
    }

    stdcingularitygac {
        process.executor = 'local'
        process.cpus = 4
        params.enable_conda = false
        params.enable_module = false
        singularity.enabled = true
        singularity.autoMounts = true
        docker.enabled = false
    }

    raven {
        process.executor = 'slurm'
        process.queue = 'prod'
        process.memory = '10GB'
        process.cpus = 4
        params.enable_conda = false
        params.enable_module = true
        singularity.enabled = false
        docker.enabled = false
        clusterOptions = '--signal B:USR2'
    }

    eprod {
        process.executor = 'slurm'
        process.queue = 'lowmem,midmem,bigmem'
        process.memory = '10GB'
        process.cpus = 4
        params.enable_conda = false
        params.enable_module = true
        singularity.enabled = false
        docker.enabled = false
        clusterOptions = '--signal B:USR2'
    }

    eprodcingularity {
        process.executor = 'slurm'
        process.queue = 'lowmem,midmem,bigmem'
        process.memory = '10GB'
        process.cpus = 4
        params.enable_conda = false
        params.enable_module = false
        singularity.enabled = true
        singularity.autoMounts = true
        docker.enabled = false
        clusterOptions = '--signal B:USR2'
    }

    cingularity {
        process.executor = 'slurm'
        process.queue = 'prod'
        process.memory = '10GB'
        process.cpus = 4
        singularity.enabled = true
        singularity.autoMounts = true
        docker.enabled = false
        params.enable_conda = false
        params.enable_module = false
        clusterOptions = '--signal B:USR2'
    }

    cingularitygac {
        process.executor = 'slurm'
        executor.$slurm.exitReadTimeout = 120000
        process.queue = 'centriflaken'
        process.cpus = 4
        singularity.enabled = true
        singularity.autoMounts = true
        docker.enabled = false
        params.enable_conda = false
        params.enable_module = false
        clusterOptions = '-n 1 --signal B:USR2'
    }

    konda {
        process.executor = 'slurm'
        process.queue = 'prod'
        process.memory = '10GB'
        process.cpus = 4
        singularity.enabled = false
        docker.enabled = false
        params.enable_conda = true
        params.enable_module = false
        clusterOptions = '--signal B:USR2'
    }

    kondagac {
        process.executor = 'slurm'
        executor.$slurm.exitReadTimeout = 120000
        process.queue = 'centriflaken'
        process.cpus = 4
        singularity.enabled = false
        docker.enabled = false
        params.enable_conda = true
        params.enable_module = false
        clusterOptions = '-n 1 --signal B:USR2'
    }

    gxkubernetes {
        process.executor = 'k8s'
        k8s.namespace = 'galaxy'
        k8s.serviceAccount = 'default'
        k8s.maxErrorRetry = 3
        k8s.pod = [
            [volumeClaim: 's3-centriflaken-claim', mountPath: '/galaxy/cfsan-centriflaken-db'],
            [volumeClaim: 's3-nextflow-claim', mountPath: '/galaxy/nf-work-dirs']
        ]
        singularity.enabled = false
        docker.enabled = true
        params.enable_conda = false
        params.enable_module = false
    }
}