new_contents: #!/usr/bin/env python
  
  # Standard packages
  import sys
  import argparse
  
  # Third-party packages
  from toil.job import Job
  
  # Package methods
  from ddb import configuration
  from ddb_ngsflow.utils import utilities
  from ddb_ngsflow import pipeline
  
  
  if __name__ == "__main__":
      parser = argparse.ArgumentParser()
      parser.add_argument('-s', '--samples_file', help="Input configuration file for samples")
      parser.add_argument('-c', '--configuration', help="Configuration file for various settings")
      Job.Runner.addToilOptions(parser)
      args = parser.parse_args()
      # args.logLevel = "INFO"
  
      sys.stdout.write("Parsing configuration data\n")
      config = configuration.configure_runtime(args.configuration)
  
      sys.stdout.write("Parsing sample data\n")
      samples = configuration.configure_samples(args.samples_file, config)
  
      root_job = Job.wrapJobFn(pipeline.spawn_batch_jobs)
  
      for sample in samples:
          diagnose_targets_job = Job.wrapJobFn(utilities.sambamba_region_coverage, config, sample, samples,
                                               "{}.recalibrated.sorted.bam".format(sample),
                                               cores=int(config['gatk']['num_cores']),
                                               memory="{}G".format(config['gatk']['max_mem']))
          root_job.addChild(diagnose_targets_job)
  
      # Start workflow execution
      Job.Runner.startToil(root_job, args)
  
subject: Add sambamba coverage script