title: Snakemake: go back and clean up temp() files
body: <p>I know variants on this have been asked before (e.g. <a href="https://groups.google.com/forum/#!topic/snakemake/4kslVBX2kew" rel="nofollow noreferrer">https://groups.google.com/forum/#!topic/snakemake/4kslVBX2kew</a>), but I don't see a definitive solution.</p>
  
  <p>If I run a long-running and complex Snakemake pipeline with '--notemp' (maybe because I'm debugging), it would be really nice to be able to subsequently run a 'cleanup' command to delete anything that would automatically have been deleted on the first run without --notemp. Is there any easy way of doing this?</p>
  
  <p>The way I'm doing this right now is to re-run after using '--forceall --touch', without '--notemp', such that everything just gets touched, and the temp files then get removed at the end. But it's not ideal to change all the timestamps. Is there a better way?</p>
  
  <p>Jon </p>