/*
 * nextflow.config – Nextflow configuration for BU SCC
 *
 * Switch executors by selecting a profile on the command line:
 *
 *   Local (default – runs on the login/compute node you are on):
 *     nextflow run multi-step.nf
 *
 *   SGE (submits each process as a batch job to the cluster):
 *     nextflow run multi-step.nf -profile sge
 */

// ---------------------------------------------------------------------------
// Default: local executor
// ---------------------------------------------------------------------------
process {
    executor = 'local'
}

// ---------------------------------------------------------------------------
// Profiles
// ---------------------------------------------------------------------------
profiles {

    // ------------------------------------------------------------------
    // sge profile – submit tasks as SGE batch jobs
    // ------------------------------------------------------------------
    sge {
        process {
            executor    = 'sge'

            // Replace 'your_project' with your SCC project name (e.g. 'tcwlab')
            clusterOptions = '-P your_project -l h_rt=00:30:00'

            // Default resource requests (override per-process with withName blocks)
            cpus   = 1
            memory = '4 GB'
            time   = '30 min'
        }

        // Example: give specific processes more resources
        // process {
        //     withName: 'ALIGN' {
        //         cpus   = 8
        //         memory = '32 GB'
        //         time   = '4 h'
        //         clusterOptions = '-P your_project -l h_rt=04:00:00'
        //     }
        // }
    }

    // ------------------------------------------------------------------
    // test profile – quick sanity check using built-in test data
    // (commonly used by nf-core pipelines)
    // ------------------------------------------------------------------
    test {
        params {
            max_cpus   = 2
            max_memory = '8 GB'
            max_time   = '1 h'
        }
    }
}