: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
metaGEM presently expects the users to have already downloaded their dateset, this can be a hurdle.
It could be useful for users to have the option to download a dataset based on an SRR ID list using fasterq-dump as described here.
Note also that users could also easily modify the downloadToy rule to download a dataset of interest. However, this requires a list of links to the individual files, which may prove cumbersome to generate.
metaGEMpresently expects the users to have already downloaded their dateset, this can be a hurdle.It could be useful for users to have the option to download a dataset based on an SRR ID list using
fasterq-dumpas described here.Note also that users could also easily modify the downloadToy rule to download a dataset of interest. However, this requires a list of links to the individual files, which may prove cumbersome to generate.