checkm cannot overwrite the folder

[sneuensc]

In the rule checkm, the folder ./checkm is problematic. If you want to rerun the pipeline, checkm breaks, as the folder ./checkm is not empty. I added to the rule end a 'rm -r ./checkm' to remove this folder after execution, allowing a rerun.

[mw55309]

Can you be a bit more explicit about when you want to do a re-run but the checkm directory is not valid?