I’m using Snakemake to write down a pipeline that includes a tool that generates a huge temporary directory, with lots of files, that is not automatically deleted after the execution is completed.
I want to set the whole directory as temporary so that it gets deleted after the pipeline is completed. However, I could only set the individual files inside the directory as temporary. Because of this, I need have a huge list of files explicitly listed in my Snakemake file and the folder itself is not deleted, so I’m left with an empty directory at the end of the pipeline.
Currently, I solved this issue by creating a rule that deletes the directory, but I don’t think this is an elegant solution.
Is there a way of setting a whole directory as a temporary output? If this isn’t possible, is there a reason for that?