souporcell_pipeline.py: ensure that logs subdirectory exists

[carandraug]

souporcell looks at whether out_dir already exists to identify if it is restarting a pipeline. This is then used to know if it needs to create the logs subdirectory.

Why is this an issue for me? I'm using mktemp -d to create separate directories for parallel souporcell_pipeline.py processes. So I'm passing an existing, but empy, out_dir to souporcell. Because souporcell uses whether out_dir exists to identify if it is resuming a previous run, it then skips the creation of the logs directory, leading to the following error later on:

Traceback (most recent call last):
  File "/opt/souporcell/souporcell_pipeline.py", line 631, in <module>
    minimap_tmp_files = remap(args, region_fastqs, all_fastqs)
  File "/opt/souporcell/souporcell_pipeline.py", line 246, in remap
    with open(args.out_dir + "/logs/minimap.err",'w') as minierr:
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/tmp-souporcell-kMN0mH/logs/minimap.err'

Actually, the whole condition is unnecessary since os.makedirs(... exist_ok=True) will already do the check and only create the directories if needed.