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params {
  config_profile_description = 'RCAC Purdue University NF config'
  config_profile_contact = 'rcac-help@purdue.edu'

  genomes {
    'b73_chr1_150000001-151000000' {
      fasta        = "${params.genomes_base}/b73_chr1_150000001-151000000.fasta"
      species      = 'Zea_mays'
    }
  }
}

// Singularity Configuration
singularity {
    enabled = true
    autoPullMode = true
    autoMounts = true
    cacheDir = "/scratch/negishi/$USER/nxf_singularity_cache"
    envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOB_ID,SINGULARITY_BINDPATH,MPLCONFIGDIR,NUMBA_CACHE_DIR'
}

// Environment Variables
env {
    SINGULARITY_CACHEDIR="/scratch/negishi/$USER/.singularity"
    OMP_NUM_THREADS = 1
    NUMBA_CACHE_DIR = "/scratch/negishi/$USER/.cache/numba"
    OPENBLAS_NUM_THREADS = 1
    PYTHONNOUSERSITE = 1
}

// Enable cleanup after pipeline execution
cleanup = true

// Profiles
profiles {
    negishilocal {
        process {
            executor = 'local'
            cache = 'lenient'
            memory = "$SLURM_MEM_PER_NODE MB"
            cpus = "$SLURM_CPUS_PER_TASK"
            process."withLabel:gpu".containerOptions = "--nv"
            _JAVA_OPTIONS="-Djava.io.tmpdir=/tmp/$SLURM_JOB_ID"
        }
    }

    negishi {
        executor {
            name = 'slurm'
            queue = 'testpbs'
            queueSize = 100
            pollInterval = '2 min'
            queueStatInterval = '5 min'
            submitRateLimit = '6/1min'
            retry.maxAttempts = 1
        }

        process {
            resourceLimits = [ cpus: 128, memory: 256.GB, time: 96.h ]
            clusterOptions = '--qos=normal --account=testpbs'
            scratch = '/tmp/$SLURM_JOB_ID'
            stageInMode = 'symlink'
            stageOutMode = 'rsync'
            cache = 'lenient'
            _JAVA_OPTIONS="-Djava.io.tmpdir=/scratch/negishi/$USER/.cache"

            // Example for setting different parameters for a specific process
            // withName: 'FASTP|MULTIQC' {
            //  cpus = 6
            //  queue = 'quick'
            //  memory = '6 GB'
            //  time = '4h'
            // }

            // Example for setting different parameters based on resource labels
            // withLabel:process_low {
            //  cpus = 2
            //  memory = '12 GB'
            //  time = '4h'
            // }
            // withLabel:process_medium {
            //  cpus = 6
            //  memory = '36 GB'
            //  time = '12h'
            // }
            // withLabel:process_high {
            //  cpus = 12
            //  memory = '72 GB'
            //  time = '16h'
            // }
        }

        timeline.enabled = true
        report.enabled = true
    }
}