The files in paper/figures/files_checkm/ are annoyingly difficult to parse. As per https://github.com/Ecogenomics/CheckM/issues/29, there is an option --tab_table that will produce a tab separated file without the fancy formatting for easy parsing. I think this can be added in these lines of code:
The files in paper/figures/files_checkm/ are annoyingly difficult to parse. As per https://github.com/Ecogenomics/CheckM/issues/29, there is an option
--tab_table
that will produce a tab separated file without the fancy formatting for easy parsing. I think this can be added in these lines of code:https://github.com/spacegraphcats/2018-paper-spacegraphcats/blob/master/pipeline-base/Snakefile#L572 https://github.com/spacegraphcats/2018-paper-spacegraphcats/blob/master/pipeline-base/Snakefile#L584 https://github.com/spacegraphcats/2018-paper-spacegraphcats/blob/master/pipeline-base/Snakefile#L596 https://github.com/spacegraphcats/2018-paper-spacegraphcats/blob/master/pipeline-base/Snakefile#L607
Which will then look like this: