old_contents: """Get log file from trimming step if file inside data["log_trimming"]"""
  
  def run(bam_file, data, dir_out):
      m = {}
      if "log_trimming" in data:
          with open(data["log_trimming"]) as inh:
              for line in inh:
                  cols = line.strip().split(":")
                  if line.find("Total reads processed:") > -1:
                      m["reads_before_trimming"] = _get_value(cols[1])
                  elif line.find("Reads with adapter:") > -1:
                      m["read_with_adapter"] = _get_value(cols[1])
                  elif line.find("Reads written") > -1:
                      m["read_pass_filter"] = _get_value(cols[1])
          return {"metrics": m, "base": data["log_trimming"]}
  
  def _get_value(information):
      return int(information.strip().split()[0].strip().replace(",", ""))
  
  
new_contents: """Get log file from trimming step if file inside data["log_trimming"]"""
  
  def run(bam_file, data, dir_out):
      m = {}
      if "log_trimming" in data:
          with open(data["log_trimming"]) as inh:
              for line in inh:
                  cols = line.strip().split(":")
                  if line.find("Total reads processed") > -1:
                      m["reads_before_trimming"] = _get_value(cols[1])
                  elif line.find("Reads with adapter") > -1:
                      m["read_with_adapter"] = _get_value(cols[1])
                  elif line.find("Reads written") > -1:
                      m["read_pass_filter"] = _get_value(cols[1])
          return {"metrics": m, "base": data["log_trimming"]}
  
  def _get_value(information):
      return int(information.strip().split()[0].strip().replace(",", ""))
  
  
subject: Fix typo in atropos log parsing