old_contents: from collections import defaultdict
  import string
  import shutil
  import glob
  
  import os.path as op
  # from bcbio.distributed.transaction import file_transaction
  from bcbio.utils import file_exists
  #, splitext_plus, safe_makedir, rbind, chdir
  
  
  def _get_template(temp):
      template =  op.normpath(op.join(op.dirname(op.realpath(__file__)), temp + ".Rmd"))
      return open(template).read()
  
  def report(out_dir=None):
      """
      create rmd template
      """
      content = _get_template("header")
      out_file = op.join(out_dir, "report-ready.Rmd")
      with open(out_file, 'w') as out_handle:
          print >>out_handle, content
  
          if file_exists(op.join(out_dir, "qsignature.ma")):
              print >>out_handle, _get_template("qsignature")
  
          print >>out_handle, _get_template("qc")
          coverage = glob.glob(op.join(out_dir, "coverage/*coverage*.bed"))
          priority = glob.glob(op.join(out_dir, "coverage/*priority*.bed"))
          print coverage
          if len(coverage) > len(priority):
              print >>out_handle, _get_template("regions")
          if glob.glob(op.join(out_dir, "variants/*tsv")):
              print >>out_handle, _get_template("variants")
  
  
new_contents: from collections import defaultdict
  import string
  import shutil
  import glob
  
  import os.path as op
  # from bcbio.distributed.transaction import file_transaction
  from bcbio.utils import file_exists
  #, splitext_plus, safe_makedir, rbind, chdir
  
  
  def _get_template(temp):
      template =  op.normpath(op.join(op.dirname(op.realpath(__file__)), temp + ".Rmd"))
      return open(template).read()
  
  def report(out_dir=None):
      """
      create rmd template
      """
      content = _get_template("header")
      out_file = op.join(out_dir, "report-ready.Rmd")
      with open(out_file, 'w') as out_handle:
          print >>out_handle, content
  
          if file_exists(op.join(out_dir, "qsignature.ma")):
              print >>out_handle, _get_template("qsignature")
  
          print >>out_handle, _get_template("qc")
          coverage = glob.glob(op.join(out_dir, "coverage/*coverage*.bed"))
          priority = glob.glob(op.join(out_dir, "coverage/*priority*.bed"))
          if len(coverage) > len(priority):
              print >>out_handle, _get_template("regions")
          if glob.glob(op.join(out_dir, "variants/*tsv")):
              print >>out_handle, _get_template("variants")
  
  
subject: Remove print