nextflow.config

params {
    project = false
    bed = false
    ref = "s3://lifebit-featured-datasets/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
    design = false
    skip_lines = 1
    test = false
    step = "1,2,4,5,6,7,8"
    run_until_n_batches = false
    samplefile = false
    index_tab = false
    indexb = false
    bindir = false
    binlist = false
    rbindir = false
    cordir = false
    gender = false
    cov = false
    covc = 50
    batch_size = 4
    target_size = 4
    start_batch = 1
    skipem = false
    cor = 0
    help = false
    samples = false
    wgs = false
    maxRetries = 1
    errorStrategy = { task.attempt <= params.maxRetries ? "retry" : "terminate" }
    queueSize = 1000
    maxForks = 45
    cpus = 1
    memory = "2.GB"
    disk = "100.GB"
    container = 'quay.io/lifebitaiorg/cnest_tomas81:dev2023_nov_standard_entrypoint'
    mode = 'copy'

    bedgz = "s3://lifebit-featured-datasets/pipelines/cnest-nf/data/hg38.1kb.baits.bed.gz"

}

process {
    withLabel: new_steps {
        container = 'tomas81/cnest:dev2024'
    }
}

executor {
  $slurm {
      queueSize = params.queueSize
      pollInterval = '30sec'
      submitRateLimit = '100 sec'
  }

  $lsf {
      queueSize = params.queueSize
      pollInterval = '30sec'
      submitRateLimit = '100 sec'
  }
}


profiles {
    test      { includeConfig 'conf/test.config' }
    standard {
        process.cpus = params.cpus
        process.memory = params.memory
        process.disk = params.disk
        process.container = params.container
        process.maxForks = params.maxForks
        process.errorStrategy = params.errorStrategy
        process.maxRetries = params.maxRetries
        docker.enabled = true
    }
    awsbatch { includeConfig 'conf/awsbatch.config' }

    slurm {
        process.executor = 'slurm'
        process.cpus = 1
        process.memory = "2.GB"
		process.time = "1h"
        process.container = 'docker://smshuai/cnest:dev2'
        process.errorStrategy = params.errorStrategy
        process.maxRetries = params.maxRetries
        singularity.enabled = true
		singularity.autoMounts = true
    }

    lsf {
        process.executor = 'lsf'
        process.cpus = 1
        process.memory = "2.GB"
        process.time = "1h"
        process.container = 'docker://smshuai/cnest:dev2'
        process.errorStrategy = params.errorStrategy
        process.maxRetries = params.maxRetries
        singularity.enabled = true
        singularity.autoMounts = true
        singularity.runOptions = '--contain'
    }

}