rm container by default #38

IMP

@@ -13,13 +13,14 @@ __doc__ = """Integrated Metaomic Pipeline.
 (____)(_/\/\_)(__)
 
 Usage:
-  IMP -m MG1 -m MG2 -t MT1 -t MT2 -o OUTPUT [--enter] [-n CONTAINER] [-e ENV] ... [COMMANDS ...]
+  IMP -m MG1 -m MG2 -t MT1 -t MT2 -o OUTPUT [--enter] [--norm] [-n CONTAINER] [-e ENV] ... [COMMANDS ...]
   IMP (-h | --help)
   IMP --version
 
 Options:
   -e ENV            Environment variable to pass to the container
   --enter           Enter the container
+  --norm            Don't delete the container after use. Useful for debugging.
   -h --help         Show this help and exit
   -m MG             Path to the metagenomics paired files (must be 2 files).
   -t MT             Path to the metatranscriptomic paired files (2 files).
@@ -96,6 +97,9 @@ if __name__ == '__main__':
         cmd += ['-it']
     # add container name and commands to pass to snakemake
     cmd += [container_name] + args['COMMANDS']
+    # rm the container by default
+    if not args['--norm']:
+        cmd += ['--rm']
     # if --enter flag is specified, change the command
     if args['--enter']:
         cmd += ['/bin/bash']