old_contents: """Assess transcript abundance in RNA-seq experiments using Cufflinks.
  
  http://cufflinks.cbcb.umd.edu/manual.html
  """
  import os
  
  from bcbio.utils import get_in, file_exists
  from bcbio.distributed.transaction import file_transaction
  from bcbio.pipeline import config_utils
  from bcbio.provenance import do
  
  
  def run(align_file, ref_file, data):
      config = data["config"]
      cmd = _get_general_options(align_file, config)
      cmd.extend(_get_no_assembly_options(ref_file, data))
      out_dir = _get_output_dir(align_file, data)
      out_file = os.path.join(out_dir, "genes.fpkm_tracking")
      if file_exists(out_file):
          return out_dir
      with file_transaction(out_dir) as tmp_out_dir:
          cmd.extend(["--output-dir", tmp_out_dir])
          cmd.extend([align_file])
          cmd = map(str, cmd)
          do.run(cmd, "Cufflinks on %s." % (align_file))
      return out_dir
  
  def _get_general_options(align_file, config):
      options = []
      cufflinks = config_utils.get_program("cufflinks", config)
      options.extend([cufflinks])
      options.extend(["--num-threads", config["algorithm"].get("num_cores", 1)])
    #  options.extend(["--quiet"])
      options.extend(["--no-update-check"])
      return options
  
  def _get_no_assembly_options(ref_file, data):
      options = []
      options.extend(["--frag-bias-correct", ref_file])
      options.extend(["--multi-read-correct"])
      options.extend(["--upper-quartile-norm"])
      gtf_file = data["genome_resources"]["rnaseq"].get("transcripts", "")
      if gtf_file:
          options.extend(["--GTF", gtf_file])
      mask_file = data["genome_resources"]["rnaseq"].get("transcripts_mask", "")
      if mask_file:
          options.extend(["--mask-file", mask_file])
  
      return options
  
  
  def _get_output_dir(align_file, data):
      config = data["config"]
      name = data["rgnames"]["sample"]
      import ipdb
      ipdb.set_trace()
      return os.path.join(get_in(data, ("dirs", "work")), "cufflinks", name)
  
new_contents: """Assess transcript abundance in RNA-seq experiments using Cufflinks.
  
  http://cufflinks.cbcb.umd.edu/manual.html
  """
  import os
  
  from bcbio.utils import get_in, file_exists
  from bcbio.distributed.transaction import file_transaction
  from bcbio.pipeline import config_utils
  from bcbio.provenance import do
  
  
  def run(align_file, ref_file, data):
      config = data["config"]
      cmd = _get_general_options(align_file, config)
      cmd.extend(_get_no_assembly_options(ref_file, data))
      out_dir = _get_output_dir(align_file, data)
      out_file = os.path.join(out_dir, "genes.fpkm_tracking")
      if file_exists(out_file):
          return out_dir
      with file_transaction(out_dir) as tmp_out_dir:
          cmd.extend(["--output-dir", tmp_out_dir])
          cmd.extend([align_file])
          cmd = map(str, cmd)
          do.run(cmd, "Cufflinks on %s." % (align_file))
      return out_dir
  
  def _get_general_options(align_file, config):
      options = []
      cufflinks = config_utils.get_program("cufflinks", config)
      options.extend([cufflinks])
      options.extend(["--num-threads", config["algorithm"].get("num_cores", 1)])
    #  options.extend(["--quiet"])
      options.extend(["--no-update-check"])
      return options
  
  def _get_no_assembly_options(ref_file, data):
      options = []
      options.extend(["--frag-bias-correct", ref_file])
      options.extend(["--multi-read-correct"])
      options.extend(["--upper-quartile-norm"])
      gtf_file = data["genome_resources"]["rnaseq"].get("transcripts", "")
      if gtf_file:
          options.extend(["--GTF", gtf_file])
      mask_file = data["genome_resources"]["rnaseq"].get("transcripts_mask", "")
      if mask_file:
          options.extend(["--mask-file", mask_file])
  
      return options
  
  
  def _get_output_dir(align_file, data):
      config = data["config"]
      name = data["rgnames"]["sample"]
      return os.path.join(get_in(data, ("dirs", "work")), "cufflinks", name)
  
subject: Remove ipdb call.