I have tried to use tasks with tophat2, but I got the following bug.
> multi.py +153
msg = 'nothing to merge for %s (expected %i files)' \
                          % (output_file_name, len(task_dirs))

This occurs because tophat2 tool uses from_work_dir feature to get the
output files.
But on the line:
output_files = [ f for f in output_files if os.path.exists(f) ]
It returnes an empty list because no real output files exists.

Did anyone else have tried this before?
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