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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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checkm cannot overwrite the folder #45

Open sneuensc opened 2 years ago

sneuensc commented 2 years ago

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 commented 1 year ago

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