code: def run_cufflinks(data):
      
      if "cufflinks" in dd.get_tools_off(data):
          return [[data]]
      work_bam = dd.get_work_bam(data)
      ref_file = dd.get_sam_ref(data)
      out_dir, fpkm_file, fpkm_isoform_file = cufflinks.run(work_bam, ref_file, data)
      data = dd.set_cufflinks_dir(data, out_dir)
      data = dd.set_fpkm(data, fpkm_file)
      data = dd.set_fpkm_isoform(data, fpkm_isoform_file)
      return [[data]]
docs: Quantitate transcript expression with Cufflinks