Deconvolution_benchmarking/nextflow.config at main · MaikTungsten/Deconvolution_benchmarking · GitHub

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/*
 * Nextflow configuration file for deconvolution benchmarking
 */

// Default parameters
params {
    input       = "$projectDir/samplesheet.csv"
    output_dir  = "$projectDir/results"
    tools       = ['BayesPrism',
                    'DWLS',
                    'GrooD',
                    'GrooD_condition',
                    'GrooD_individual',
                    'MuSiC',
                    'Scaden']

    // Script paths
    scripts {
        // Pipeline scripts
        preprocess  = "$projectDir/bin/preprocess.py"
        evaluate    = "$projectDir/bin/evaluate.py"
        visualize   = "$projectDir/bin/visualize.py"

        // Tool scripts
        bayesprism  = "$projectDir/bin/tools/bayesprism.R"
        dwls        = "$projectDir/bin/tools/dwls.py"
        grood       = "$projectDir/bin/tools/grood.py"
        grood_cond  = "$projectDir/bin/tools/grood_cond.py"
        grood_indiv = "$projectDir/bin/tools/grood_indiv.py"
        music       = "$projectDir/bin/tools/music.R"
        scaden      = "$projectDir/bin/tools/scaden.py"
    }

    // Tool-specific parameters
    bayesprism {
        cpu = 1
        memory = '16 GB'
    }

    dwls {
        cpu = 1
        memory = '16 GB'
    }

    grood {
        cpu = 8
        memory = '16 GB'
    }

    music {
        cpu = 1
        memory = '16 GB'
    }

    scaden {
        cpu = 1
        memory = '16 GB'
    }
}

// Process-specific settings
process {
    cache = true

    withName: 'BAYESPRISM' {
        cpus = params.bayesprism.cpu
        memory = params.bayesprism.memory
    }

    withName: 'DWLS' {
        cpus = params.dwls.cpu
        memory = params.dwls.memory
    }

    withName: 'GROOD' {
        cpus = params.grood.cpu
        memory = params.grood.memory
    }

    withName: 'GROOD_COND' {
        cpus = params.grood.cpu
        memory = params.grood.memory
    }

    withName: 'GROOD_INDIV' {
        cpus = params.grood.cpu
        memory = params.grood.memory
    }

    withName: 'MUSIC' {
        cpus = params.music.cpu
        memory = params.music.memory
    }

    withName: 'SCADEN' {
        cpus = params.scaden.cpu
        memory = params.scaden.memory
    }
}

executor {
  cpus = 64
}

// Execution profiles
profiles {
    docker {
        docker.enabled = true
        process.container = 'deconv-benchmark:latest'
    }
}

// Cleanup after successful runs
// cleanup = true