Add protected and temporary to the relevant outputs

[JihedC]

There are a lot of files that can be removed once the pipeline is finished. Here

[JihedC]

adding temp() to the unnecessary files worked well, but when I added protected() to the files required by the rule_all and rerun the pipeline for whatever reason, snakelike throws an error.

[JihedC]

protected() prevents Snakemake from rewriting the file, so it makes senses that it throws an error when rerun...