params {
  refSource = "aws"
}

workDir = 's3://gudmap-rbk.output/work'
aws.client.storageEncryption = 'AES256'
aws {
  region = 'us-east-2'
  batch {
    cliPath = '/home/ec2-user/miniconda/bin/aws'
  }
}

process {
  executor = 'awsbatch'
  cpus = 1
  memory = '1 GB'

  withName: trackStart {
    cpus = 1
    memory = '1 GB'
  }
  withName: getBag {
    cpus = 1
    memory = '1 GB'
  }
  withName: getData {
    cpus = 1
    memory = '1 GB'
  }
  withName: parseMetadata {
    cpus = 15
    memory = '1 GB'
  }
  withName: trimData {
    cpus = 20
    memory = '2 GB'
  }
  withName: getRefInfer {
    cpus = 1
    memory = '1 GB'
  }
  withName: downsampleData {
    cpus = 1
    memory = '1 GB'
  }
  withName: alignSampleData {
    cpus = 50
    memory = '5 GB'
  }
  withName: inferMetadata {
    cpus = 5
    memory = '1 GB'
  }
  withName: getRef {
    cpus = 1
    memory = '1 GB'
  }
  withName: alignData {
    cpus = 50
    memory = '10 GB'
  }
  withName: dedupData {
    cpus = 5
    memory = '20 GB'
  }
  withName: countData {
    cpus = 2
    memory = '5 GB'
  }
  withName: makeBigWig {
    cpus = 15
    memory = '5 GB'
  }
  withName: fastqc {
    cpus = 1
    memory = '1 GB'
  }
  withName: dataQC {
    cpus = 15
    memory = '2 GB'
  }
  withName: aggrQC {
    cpus = 2
    memory = '1 GB'
  }
  withName: outputBag {
    cpus = 1
    memory = '1 GB'
  }
  withName: uploadInputBag {
    cpus = 1
    memory = '1 GB'
  }
  withName: uploadExecutionRun {
    cpus = 1
    memory = '1 GB'
  }
}