old_contents: import glob
  import logging
  import os
  import subprocess
  from plugins import BaseAssessment
  from yapsy.IPlugin import IPlugin
  import asmtypes
  
  class QuastAssessment(BaseAssessment, IPlugin):
      new_version = True
  
      def run(self):
  
          contigsets = self.data.contigsets
  
          for i,c, in enumerate(contigsets):
              c['tags'].append('quast-{}'.format(i+1))
          contigfiles = self.data.contigfiles
          if len(contigsets) == 0: #Check for scaffolds
              contigsets = self.data.scaffoldsets
              contigfiles = self.data.scaffoldfiles
              scaffolds = True
              assert len(contigsets) != 0
          else: scaffolds = False
  
          ref = self.initial_data.referencefiles or None
          
          cmd_args = [os.path.join(os.getcwd(),self.executable), 
                      '--min-contig', self.min_contig,
                      '-o', self.outpath,
                      '--gene-finding']
          if scaffolds: cmd_args.append('--scaffolds')
  
          #### Add Reference ####
          if ref:
              rfile = ref[0]
              cmd_args += ['-R', rfile, '--gage']
  
          #### Add Contig files ####
          cmd_args += contigfiles
          cmd_args += ['-l', '"{}"'.format(', '.join([cset.name for cset in contigsets]))]
          
  
          #### Run Quast ####
          self.arast_popen(cmd_args)
          
          output = {}
          report = os.path.join(self.outpath, 'report.txt')
          if not os.path.exists(report):
              print 'No Quast Output'
              report = None
          else: output['report'] = report
          return output
      
  
new_contents: import glob
  import logging
  import os
  import subprocess
  from plugins import BaseAssessment
  from yapsy.IPlugin import IPlugin
  import asmtypes
  
  class QuastAssessment(BaseAssessment, IPlugin):
      new_version = True
  
      def run(self):
  
          contigsets = self.data.contigsets
  
          for i,c, in enumerate(contigsets):
              c['tags'].append('quast-{}'.format(i+1))
          contigfiles = self.data.contigfiles
          if len(contigsets) == 0: #Check for scaffolds
              contigsets = self.data.scaffoldsets
              contigfiles = self.data.scaffoldfiles
              scaffolds = True
              assert len(contigsets) != 0
          else: scaffolds = False
  
          ref = self.initial_data.referencefiles or None
          
          cmd_args = [os.path.join(os.getcwd(),self.executable),
                      '--threads', self.process_threads_allowed,
                      '--min-contig', self.min_contig,
                      '-o', self.outpath,
                      '--gene-finding']
          if scaffolds: cmd_args.append('--scaffolds')
  
          #### Add Reference ####
          if ref:
              rfile = ref[0]
              cmd_args += ['-R', rfile, '--gage']
  
          #### Add Contig files ####
          cmd_args += contigfiles
          cmd_args += ['-l', '"{}"'.format(', '.join([cset.name for cset in contigsets]))]
          
  
          #### Run Quast ####
          self.arast_popen(cmd_args)
          
          output = {}
          report = os.path.join(self.outpath, 'report.txt')
          if not os.path.exists(report):
              print 'No Quast Output'
              report = None
          else: output['report'] = report
          return output
      
  
subject: fix thread number for quast