code: def choose_samples(samples, force):
      
  
      ## hold samples that pass
      subsamples = []
      ## filter the samples again
      if not force:
          for sample in samples:
              if sample.stats.state >= 2:
                  print("""\
      Skipping Sample {}; Already filtered. Use force argument to overwrite.\
      """.format(sample.name))
              elif not sample.stats.reads_raw:
                  print("""\
      Skipping Sample {}; No reads found in file {}\
      """.format(sample.name, sample.files.fastqs))
              else:
                  subsamples.append(sample)
  
      else:
          for sample in samples:
              if not sample.stats.reads_raw:
                  print("""\
      Skipping Sample {}; No reads found in file {}\
      """.format(sample.name, sample.files.fastqs))
              else:
                  subsamples.append(sample)
      return subsamples
docs: filter out samples that are already done with this step, unless force