search

franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
189 stars 41 forks source link

Fix an error in kallisto2concut #95

Closed Xentrics closed 2 years ago

Xentrics commented 2 years ago

The bash code of rule kallisto2concut was missing a directory '/'

franciscozorrilla commented 2 years ago

Thanks for the fix, although doesn't the {input} variable already have a slash at the end in the Snakefile by default? I will accept this change anyways, as I understand that a double slash would be harmless.

https://github.com/franciscozorrilla/metaGEM/blob/9796e3ab98e38afcd26147fe58df32190002810f/Snakefile#L594-L619

Xentrics commented 2 years ago

Strangely, it did not in my case. While I do see that {input} should already have a backslash, but it did not translate into the shell command. I suspect that there might be something related to the Snakemake replacement mechanism. But double slash is almost always the easiest solution to such a problem :).