new_contents: #!/usr/bin/env python
  
  import os
  import sys
  import pandas as pd
  from glob import glob
  import subprocess
  
  def main():
      if len(sys.argv) != 3:
          print("Usage: extract_logs_from_nextflow.py <nextflow_trace_file> <task_tag>:<stderr|stdout|both>",file=sys.stderr)
          
      # Load Nextflow trace
      nextflow_trace = pd.read_csv(sys.argv[1],sep="\t")
      #Get task you are interested in and whether you want stderr/stdout/both
      # Format <task>:<stderr|stdout|both>
      task_id,output_type = sys.argv[2].split(":")
  
      #Create dirs
      out_dir="nextflow_logs/{}".format(task_id)
      os.makedirs(out_dir)
  
      # Subset tasks of interest
      my_tasks = list(nextflow_trace[ (nextflow_trace.process == task_id) ][["hash","tag","status"]].itertuples(index=False,name=None))
  
      if len(my_tasks) == 0:
          print("No tasks were found",file=sys.stderr)
  
      # Iterate through tasks
      for t_hash,t_tag,t_status in my_tasks:
          task_dir= get_hash_directory(t_hash)
          if not task_dir:
              print("Error: work/{}* directory was not found".format(t_hash))
              continue
          print("{}: {}".format(t_tag,task_dir))
  
          out_prefix="{}_{}_{}".format(t_tag,t_status[0],t_hash.replace("/","_"))
  
          if output_type != "stderr":
              copy_file_into_dir("{}/.command.out".format(task_dir),out_dir,prefix=out_prefix)
          if output_type != "stdout":
              copy_file_into_dir("{}/.command.err".format(task_dir),out_dir,prefix=out_prefix)
  
  # Helping functions
  def get_hash_directory( h ):
      my_task_dir = None
      matching_dirs = glob("work/{}*".format(h))
      if len(matching_dirs) == 1:
          my_task_dir = matching_dirs[0]
      return my_task_dir
  
  def copy_file_into_dir(my_file,my_dir,prefix=""):
      print("\t{}".format(my_file))
      subprocess.check_call(["cp",my_file,"{}/{}.{}".format(my_dir,prefix,my_file[-3:])])
  
  if __name__ == '__main__':
      main()
  
subject: Add script to extract stderr and stout from nextflow