nextflow.config

/**
 * This configuration file specifies a default pipeline setup for running brain
 * decoding on a local machine with a GPU. (See the project README for minimal
 * computing specs to run the pipeline.)
 *
 * While this pipeline does *work* running on a local machine, we recommend
 * deploying on a high-performance cluster. See the file
 * `nextflow.slurm.config` for an example deployment configuration for SLURM
 * clusters.
 */
process {
    executor = "local"

    /**
     * Pipeline processes are assigned "labels" according to their
     * computational requirements. Here we can specify the actual effects of
     * each label when the pipeline runs on your system.
     *
     * This first label, `small`, describes simple tasks which can easily run
     * on a single CPU with minimal RAM -- e.g. downloading a file.
     */
    withLabel: 'small' {
        executor = 'local'
        memory = '1G'
    }

    /**
     * `medium` describes tasks which require moderate host memory, e.g.
     * loading brain images and learning linear regression models.
     */
    withLabel: 'medium' {
        time = '1d'
        memory = '8G'
    }

    /**
     * `gpu_medium` describes tasks which require a GPU with moderate memory
     * and moderate host RAM, for e.g. holding a dataset in memory and running
     * neural network feed-forward inference.
     */
    withLabel: 'gpu_medium' {
        containerOptions = "--nv"
    }

    /**
     * `gpu_large` describes tasks which require a GPU with lots of memory and
     * large host RAM, for e.g. holding a training dataset in memory and
     * running neural network training.
     */
    withLabel: 'gpu_large' {
        containerOptions = "--nv"
        time = '1d'
        memory = '16G'
        containerOptions = "--nv"
    }
}

/**
 * You can limit the maximum number of parallel executing processes using
 * the variable below. This may be relevant when running with a single GPU,
 * for example.
 */
executor {
    queueSize = 1
}

// There should be no need to edit below this line.
//////////////////////////////////////////

params.bert_container = "library://jon/default/bert:base-gpu"
params.structural_probes_container = "library://jon/default/structural-probes:latest"
params.decoding_container = "library://jon/default/nn-decoding:emnlp2019"

singularity {
    enabled = true
    envWhitelist = "CUDA_VISIBLE_DEVICES"
    autoMounts = true
}
report.enabled = true