profiles {
    
    standard {
        process.executor = 'local'
        params.cores = 1
        params.python_module = ""
        params.mummer_module = ""
        params.skesa_module = ""
        params.bedtools_module = ""
        params.mash_module = ""
        params.bbtools_module = ""
    }
    
    slurmHPC {
        process.executor = 'slurm'
        params.cores = 20
        params.python_module = "/nfs/software/modules/python/3.8.1"
        params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
        params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
        params.bedtools_module = "/nfs/sw/Modules/bedtools"
        params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
        params.mash_module = "/nfs/software/modules/mash/2.3"
        params.trim_name = "_contigs_skesa"
    }
    
    slurmHPC_int {
        process.executor = 'local'
        params.cores = 20
        params.python_module = "/nfs/software/modules/python/3.8.1"
        params.mummer_module = "/nfs/software/modules/mummer/4.0.0"
        params.skesa_module = "/nfs/software/modules/skesa/2.5.0"
        params.bedtools_module = "/nfs/sw/Modules/bedtools"
        params.bbtools_module = "/nfs/software/modules/bbtools/38.94"
        params.mash_module = "/nfs/software/modules/mash/2.3"
        params.trim_name = "_contigs_skesa"
    }
    
    slurm_nm {
        process.executor = 'slurm'
        params.cores = 1
        params.python_module = ""
        params.mummer_module = ""
        params.skesa_module = ""
        params.bedtools_module = ""
        params.bbtools_module = ""
        params.mash_module = ""
        params.trim_name = ""
    }
    
    standard_conda {
        conda.enabled = true
        conda.cacheDir = "${projectDir}/CSP2_env"
        process.conda = "${projectDir}/conf/CSP2.yaml"
        
        process.executor = 'local'
        params.cores = 1
        params.python_module = ""
        params.mummer_module = ""
        params.skesa_module = ""
        params.bedtools_module = ""
        params.bbtools_module = ""
        params.mash_module = ""
        params.trim_name = ""
    }

    slurm_conda {
        conda.enabled = true
        conda.cacheDir = "${projectDir}/CSP2_env"
        process.conda = "${projectDir}/conf/CSP2.yaml"
        
        process.executor = 'slurm'
        params.cores = 1
        params.python_module = ""
        params.mummer_module = ""
        params.skesa_module = ""
        params.bedtools_module = ""
        params.bbtools_module = ""
        params.mash_module = ""
        params.trim_name = ""
    }
    
    csp2_galaxy {
        conda.enabled = true
        conda.useMicromamba = true
        conda.cacheDir = "${projectDir}/CSP2_env"
        process.conda = "${projectDir}/conf/CSP2.yaml"
        
        process.queue = "ondemand-small"

        executor.$slurm.exitReadTimeout = 120000

        process.executor = 'slurm'
        params.cores = 1
        params.python_module = ""
        params.mummer_module = ""
        params.skesa_module = ""
        params.bedtools_module = ""
        params.bbtools_module = ""
        params.mash_module = ""
        params.trim_name = ""
    }
}