old_contents: #!/usr/bin/env python
  
  #--------------------------------------
  #
  #        snippy_core_wrapper.py
  #
  # This is an intermediary script between snippy-core.xml and snippy-core
  # It:
  #   - Copys the supplied zipped snippy output files to the working dir
  #   - Untars them to their datafile name
  #   - Builds the snippy-core command
  #   - Runs the snippy-core command
  #
  #--------------------------------------
  
  import os
  import sys
  import argparse
  import subprocess
  from shutil import copyfile
  
  def main():
      parser = argparse.ArgumentParser()
      parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
      parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
      args = parser.parse_args()
  
      snippy_core_command_line = ['snippy-core', '--ref', args.ref]
  
      for indir in args.indirs.split(','):
          base_name = os.path.basename(indir)
          copyfile(indir, base_name)
          subprocess.Popen(['tar', '-xf', base_name])
  
      extracted_dirs = [f.path for f in os.listdir('.') if os.path.isdir(f) ]
  
      for extracted_dir in extracted_dirs:
          snippy_core_command_line.append(extracted_dir)
  
      subprocess.Popen(snippy_core_command_line)
  
  if __name__ == '__main__':
      main()
  
new_contents: #!/usr/bin/env python
  
  # --------------------------------------
  #
  #        snippy_core_wrapper.py
  #
  # This is an intermediary script between snippy-core.xml and snippy-core
  # It:
  #   - Copys the supplied zipped snippy output files to the working dir
  #   - Untars them to their datafile name
  #   - Builds the snippy-core command
  #   - Runs the snippy-core command
  #
  # --------------------------------------
  
  import argparse
  import os
  import subprocess
  from shutil import copyfile
  
  def main():
  
  
      parser = argparse.ArgumentParser()
      parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
      parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
      args = parser.parse_args()
  
      snippy_core_command_line = ['snippy-core', '--ref', args.ref]
  
      for input_dataset in args.indirs.split(','):
          base_name = os.path.basename(input_dataset)
          copyfile(input_dataset, base_name)
          subprocess.Popen(['tar', '-xf', base_name])
  
      extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
      for extracted_dir in extracted_dirs:
          snippy_core_command_line.append(extracted_dir)
  
      subprocess.Popen(snippy_core_command_line).wait()
  
  
  if __name__ == '__main__':
      main()
  
subject: Update snippy_core_wrapper.py