Configuration File

The config file is a simple text file with a list of key-value pairs. You can use the config file to set the pipeline's parameters. The config file is optional, but it is recommended to use it to avoid typing the same parameters over and over again. The config file is specified with the -c option. For example:

# get an example config file
wget -O example_custom.config "https://raw.githubusercontent.com/deng-lab/viroprofiler/main/custom.config"

# modify the config file using your favorite text editor ...
# run with config
nextflow run deng-lab/viroprofiler -c example_custom.config

Default configuration

profiles {
    singularity {
        // Please modify this singularity run options to fit your needs
        // If your data or database is stored in a different disk, you may need to mount it to the container using the `-B /path/to/data:/path/to/data` option
        // singularity.runOptions = "--writable-tmpfs -B /path/to/data:/path/to/data"
    }

    // `slurm_denglab` is the default profile used in DengLab at HMGU
    slurm_denglab {
        process.executor       = 'slurm'    // change this to your cluster executor
        process.cpus           = 1
        process.memory         = '8 GB'
        process.queue          = 'normal_q'  // change this to your queue
        process.time           = '120 h'
    }
    // Please specify your own profile here
    // and set the parameters accordingly to your local system
    // e.g.:
    // your_own_profile {
    //     process.executor = 'sge'
    //     process.cpus     = 4
    //     process.memory   = '8 GB'
    // }
}

process {
    withName: FASTP {
        // Non-default parameters for can be set here using `ext.args`
        ext.args = "-f 15 -t 1 -F 15 -T 1 --detect_adapter_for_pe -p -n 1 -l 30 -5 -W 4 -M 20 -r -c -g -x"
        cpus = 4
        memory = "50 GB"
    }

    withName: FASTQC {
        ext.args = '--quiet'
    }

    withName: DECONTAM {
        ext.args = 'maxindel=1 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 pigz=True untrim'
        cpus = 4
        memory = "80 GB"
    }

    withName: SPADES {
        ext.args = "--meta"
        cpus = 4
        memory = "100 GB"
    }

    withName: CONTIGLIB {
        cpus = 4
        memory = "40 GB"
    }

    withName: CHECKV {
        cpus = 1
        memory = "30 GB"
    }

    withName: CONTIGLIB_CLUSTER {
        cpus = 2
        memory = "40 GB"
    }

    withName: MAPPING2CONTIGS {
        cpus = 2
        memory = "60 GB"
    }

    withName: ABUNDANCE {
        cpus = 2
        memory = "40 GB"
    }

    withName: DVF {
        cpus = 8
        memory = "60 GB"
    }

    withName: VAMB {
        cpus = 8 
        memory = "120 GB"
    }

    withName: VRHYME {
        ext.args = "--method longest"
        cpus = 2
        memory = "20 GB"
    }

    withName: NRSEQS {
        cpus = 4
        memory = "80 GB"
    }

    withName: MICOMPLETEDB {
        cpus = 8
        memory = "80 GB"
    }

    withName: VOGDB {
        cpus = 4
        memory = "40 GB"
    }

    withName: EMAPPER {
        cpus = 22
        memory = "300 GB"
    }

    withName: PHAMB_RF {
        cpus = 8
        memory = "80 GB"
    }

    withName: VIRSORTER2 {
        cpus = 4
        memory = "100 GB"
    }

    withName: DRAMV {
        cpus = 1
        memory = "200 GB"
    }

    withName: TAXONOMY_VCONTACT {
        cpus = 4
        memory = "100 GB"
    }

    withName: TAXONOMY_MMSEQS {
        cpus = 4
        memory = "120 GB"
    }

    withName: VIRALHOST_IPHOP {
        cpus = 12
        memory = "300 GB"
    }

    withName: BACPHLIP {
        ext.args = "--multi_fasta"
        cpus = 4
        memory = "80 GB"
    }

    withName: REPLIDEC {
        cpus = 4
        memory = "80 GB"
    }
}