nextflow.config

cleanup = true

params {
    out_dir = './output'
    report_dir = './reports'
    custom_config_version       = 'master'
    custom_config_base          = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"

    try {
        includeConfig "${params.custom_config_base}/conf/sanger.config"
    } catch (Exception e) {
        System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/conf/sanger.config")
    }
}

profiles {
  local {
    includeConfig 'conf/local.config'
    process.executor = 'local'
  }

  lsf {
    includeConfig 'conf/lsf.config'
  }
}

process {
    errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
    maxRetries = 5

    cpus = { 8 * task.attempt }
    memory = { 80.GB * task.attempt }

    withName: BIOINFOTONGLI_BIOFORMATS2RAW {
        ext.args = [
            '--no-hcs',
            '--tile_height=2048',
            '--tile_width=2048',
            ].join(' ')
    }
    withName: QCAlignment {
        ext.args = [
            '--channels [0,5,10,15,20,25,30]',
            ].join(' ')
    }
}

includeConfig 'subworkflows/sanger/bioinfotongli/to_ome_tiff/nextflow.config'