At the moment we are keeping all the files from the workflow in the output. I think some of the files can be deleted, especially from the data intake module. I suggest that any files that we want to remove, we store in a directory called ./tmp and we mark the outputs with the 'temp' function (https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-temp-and-protected-files). @hverbruggen - do you know what rules produce only temporary files.
At the moment we are keeping all the files from the workflow in the output. I think some of the files can be deleted, especially from the data intake module. I suggest that any files that we want to remove, we store in a directory called ./tmp and we mark the outputs with the 'temp' function (https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-temp-and-protected-files). @hverbruggen - do you know what rules produce only temporary files.