nextflow.config

params{
//default parameters that are inputs to the pipeline
input = "input/SAL_CA55*.fasta"
kingdom = "Bacterial"
gram = "neg" //todo add in null for viruses etc.
help = false
outdir = "results"
multiqc_config = "$baseDir/conf/multiqc_config.yaml"
kraken_db = "/home/tom/lodestone-ci/k2_pluspf_16gb/"
pangenome = "panaroo"
localisation = "psortb"
}

profiles{
    slurm {
        process {
        executor = "slurm"
        queue = "compute"
        memory = "8GB"
        cpus = 1
        time = "1h"
        queue = "htc"

        withLabel:multithreaded{
            cpus = 40
            memory = "72GB"
            queue = "compute"
        }
    }

    executor {
        queueSize = 20
        }
    }
    
    standard {
        process {
            cpus = 1

        withLabel:multithreaded{
            cpus = 8
        }
        }
    }
    
    singularity {
        singularity.enabled = true
    }

    conda {
        params.enable_conda = true
        conda.useMamba = true
        process.conda = '/home/tom/mambaforge/envs/recipient'
    }
}