Nextflow pipeline to test if the CUDA_VISIBLE_DEVICES is set.

main.nf

#!/usr/bin/env nextflow

modes = [0, 1, 2, 3, 4]
process gpu_output {
    echo true

    script:
    """
    echo \$CUDA_VISIBLE_DEVICES
    """
}

nextflow.config

profiles {
    gpu {
        singularity.runOptions = '--nv'
        process.queue = 'gpu'
        process.clusterOptions = '--gres=gpu:gtx:1'
        env.CUDA_VISIBLE_DEVICES='\$CUDA_VISIBLE_DEVICES'
    }
}