nextflow.config

params.kradb="/blue/bphl-florida/share/kraken_databases"
params.krdbName = "maxikraken2_1903_140GB"

params {
    // Pipeline version
    version = '1.0.0dev'
    // default assembler
    asb_tool = 'dragonflye'
    help = false
    // Canu parameters
    //useGrid=false
    //rawErrorRate = 0.500
    //correctedErrorRate = 0.144
    //minReadLength = 1000
    //minOverlapLength = 500
    //params.canu_options = false
    //unicycler parameter
    mode = 'normal'
}

process {
    withName: kraken {
        container = '/apps/staphb-toolkit/containers/kraken2_2.0.8-beta.sif'
        cpus = 8       
    }
    
    withName: krakenMax {
        container = '/apps/staphb-toolkit/containers/kraken2_2.1.2-no-db.sif'
        cpus = 16
        memory = '160 GB'
        time = '30 min'
    }
    withName: amrfinderplus {
        container = '/apps/staphb-toolkit/containers/ncbi-amrfinderplus_3.10.1.sif'
        cpus = 8    
    }

    withName:kaiju {
        module = 'kaiju/1.7.2'
        cpus = 8

    }
    
    withName:mash {
        container = '/apps/staphb-toolkit/containers/mash_2.2.sif'
        cpus = 8

    }

    withName:hb_unicycler {
        module = 'unicycler/0.4.8'
        cpus = 8
        memory = '64 GB'  

    }
   
    withName:hb_dragonflye {
        module = 'dragonflye/1.0.12'
        cpus = 8
        memory = '16 GB'

    }
    
    withName:pilon {
        module = 'pilon/1.24'
        //pilon_1.23.0.sif
        //container = '/apps/staphb-toolkit/containers/pilon_1.23.0.sif' 
        cpus = 16
        //memory = '64 GB'
    }

    withName:hb_canu {
        //module = 'canu'
        module = 'gnuplot/5.4.1'
       // module  = 'apptainer'
        container = '/apps/staphb-toolkit/containers/canu-2.0.sif'
        //cpus = 16
        //memory = '16 GB'
    }
    withName:minimap {
        //module = 'minimap2/2.24'
        container = '/apps/staphb-toolkit/containers/minimap2_2.18.sif'
        //module = 'samtools/1.15'
        //container = '/apps/staphb-toolkit/containers/samtools_1.12.sif'
        //module = 'apptainer/1.1.0'
    }

    withName:bwa_aln {
        module= 'bwa/0.7.17'
        cpus = 8
        memory = '32 GB'
    }

    withName:samtools_conv {
                                                                                                                                                                              
        container = '/apps/staphb-toolkit/containers/samtools_1.12.sif'
    }
    
    withName:quast {
        module = 'quast/5.0.2'
    }
    
    withName:bakta {
        module = 'bakta/1.3.3'
        cpus = 8       
    }
/*
    withName:refseq_dwld {
        module = 'python'
    }
*/
}

//singularity.enabled = true

singularity {
    enabled = true
}

manifest {
  homePage = 'https://github.com/BPHL-Molecular/flisochar'
  description = 'Florida Isolate Characterization Pipeline.'
  mainScript = 'main.nf' // or mainScript = 'flisochar.nf'
 
}

mail {
    smtp.host = 'smtp.gmail.com'
    smtp.port = 25
}  
//module  = 'apptainer'