modkitopt/nextflow.config at main · comprna/modkitopt · GitHub

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params {
    //--------------------------------------------------------------------------
    // Inputs
    //--------------------------------------------------------------------------
    modbam            = null                // Path to modBAM file output by mod caller
    mod_type          = null                // Type of modification
    modkit            = null                // Path to modkit executable
    fasta             = null                // Reference fasta file for modkit
    annotation        = null                // Annotation file for t2g
    truth_sites       = null                // Ground truth modification sites
    filter_thresholds = [0.5, 0.75, 0.9,
                         0.95, 0.99, 0.995] // Modkit --filter_threshold values to test
    mod_thresholds    = [0.5, 0.75, 0.9,
                         0.95, 0.99, 0.995] // Modkit --mod_threshold values to test
    top_outdir        = "results"           // Where to write output to
    help              = null                // Initialise help message
    install           = false               // Whether to run in install mode
    demo              = false               // Whether to run demo

    //--------------------------------------------------------------------------
    // Resources
    //--------------------------------------------------------------------------
    default_cpus      = 1         // Default CPUs to request per process
    default_memory    = '8GB'     // Default memory to request per process
    default_time      = '1h'      // Default time to request per process
    filter_cpus       = 8         // Default CPUs to request for samtools filter
    sort_cpus         = 8         // Default CPUs to request for samtools sort
    index_cpus        = 4         // Default CPUs to request for samtools index
    pileup_cpus       = 8         // Default CPUs to request for modkit pileup
    pileup_memory     = '30GB'    // Default memory to request for modkit pileup
    pileup_time       = '1h'      // Default time to request for modkit pileup
    t2g_memory        = '30GB'    // Default memory to request for t2g
    t2g_disk          = '5GB'     // Default job filesystem disk space to request for t2g
    hpc_queue         = null      // User to override this if running in HPC environ
    hpc_project       = null      // User to override this if running in HPC environ
    hpc_storage       = null      // User to override this if running in HPC environ
}

profiles {
    local {
        includeConfig 'profiles/local.config'
    }

    slurm {
        includeConfig 'profiles/slurm.config'
    }

    pbs {
        includeConfig 'profiles/pbs.config'
    }

    pbspro {
        includeConfig 'profiles/pbspro.config'
    }

    // default profile if profile not specified
    standard {
        includeConfig 'profiles/local.config'
    }
}