new_contents: #!/bin/env python
  
  """ pipeline_quickstart_config.py 
  
      -Configuration file to set input files, directories and parameters 
      specific to pipeline_quickstart.py
  =============================================================================
  """
  
  import os
  import WitsgwasScripts as SC 
  import QuickstartUserInput as I
  
  
  # This section is used by the pipeline_quickstart.py to specify input data and 
  # working directories.
  
  # Required inputs:
  # 1. path to input1 
  # 2. path to input2
  # 3. input3
  
  '''
  note: project name will be used by the pipeline to generate a 
  time stamped output directory '''
  
  
  working_files = {
  }
  
  
  # This OPTIONAL section is used by the pipeline_quickstart.py to submit preselected user cutoffs
  
  preselected_cutoff = {
  }
  
  
  
  # This section is used by the pipeline_quickstart.py to specify configuration options 
  # for itself (pipeline_quickstart.py) as well as Rubra. 
  
  # Rubra variables:
  #  - logDir: the directory where batch queue scripts, stdout and sterr dumps are stored.
  #  - logFile: the file used to log all jobs that are run.
  #  - style: the default style, one of 'flowchart', 'print', 'run', 'touchfiles'. Can be 
  #      overridden by specifying --style on the command line.
  #  - procs: the number of python processes to run simultaneously. This determines the
  #      maximum parallelism of the pipeline. For distributed jobs it also constrains the
  #      maximum total jobs submitted to the queue at any one time.
  #  - verbosity: one of 0 (quiet), 1 (normal), 2 (chatty). Can be overridden by specifying
  #      --verbose on the command line.
  #  - end: the desired tasks to be run. Rubra will also run all tasks which are dependencies 
  #      of these tasks. Can be overridden by specifying --end on the command line.
  #  - force: tasks which will be forced to run, regardless of timestamps. Can be overridden
  #      by supplying --force on the command line.
  #  - rebuild: one of 'fromstart','fromend'. Whether to calculate which dependencies will
  #      be rerun by working back from an end task to the latest up-to-date task, or forward
  #      from the earliest out-of-date task. 'fromstart' is the most conservative and 
  #      commonly used as it brings all intermediate tasks up to date.
  
  
  # pipeline_quickstart variables:
  # nothing at this stage, but could be used to add more features in future
  
  pipeline = {
      'logDir': os.path.join(SC.CURRENT_PROJECT_DIR, "log_quickstart"),
      'logFile': 'pipeline_quickstart.log',
      'style': 'print',
      'procs': 30,
      'verbose': 1,
      'end': ['quickstart_end_task' 
              ],
      'force': [],
      'rebuild' : "fromstart",
  
      'restrict_samples': False,
      'allowed_samples': []
      
  }
  
subject: Create pipeline_quickstart_config.py