nextflow.config

// This is an example file, please adapt it to your resources.
// For more information see tool documentation and Nextflow documentation.


// CONTAINER SETTINGS:
singularity {
    enabled = true
    // cacheDir = ''            // to set a directory where to download the container file 
    autoMounts = true           // to automatically mount host paths in the executed container
}
// docker {
    // enabled = true
// }

// EXECUTOR SETTINGS:
executor {
    name = ''                   // e.g. 'sge', 'local'
    // queueSize =              // e.g. 4, to limit the number of processes handled in parallel
    // cpus =                   // e.g. 3, to limit the CPU resources when using the 'local' executor
}

process {
    container = 'vibpsb/ksrates:latest'        // to use the ksrates container (not needed if all dependencies are locally installed)

    // Specify memory and number of threads for processes submitted to the cluster 
    // It is advised to provide higher computational power to wgdParalogs and wgdOrthologs 
    withName: 'wgdParalogs' {
        cpus =                  // e.g. 8 on a cluster or 2 on local computer
        penv = ''               // e.g. 'serial'
        memory = ''             // e.g. '16GB'
        clusterOptions = ''     // e.g. '-l h_vmem=2G'
    }

    withName: 'wgdOrthologs' {
        cpus =                  // e.g. 8 on a cluster or 2 on local computer
        penv = ''               // e.g. 'serial'
        memory = ''             // e.g. '16GB'
        clusterOptions = ''     // e.g. '-l h_vmem=2G'
    }

    withName: 'estimatePeaks' {
        memory = ''             // e.g. '2GB'
        clusterOptions = ''     // e.g. '-l h_vmem=2G'
    }

    withName: 'paralogsAnalyses' {
        memory = ''             // e.g. '8GB'
        clusterOptions = ''     // e.g. '-l h_vmem=8G'
    }
    
    withName: 'plotOrthologDistrib' {
        memory = ''             // e.g. '2GB'
        clusterOptions = ''     // e.g. '-l h_vmem=2G'
    }
}


// OTHER SETTINGS:
// env.SOME_ENV_VARIABLE = ''