CLI Workflows automate common tasks in MiGA. Currently implemented workflows include:
It is possible to concatenate workflows in the same project. First, run the first workflow as described in the documentation. For example:
miga quality_wf -o my_project /path/to/genomes/*.fna
Next, execute any additional steps without specifying the input files, and using the same output directory. For example:
miga classify_wf -o my_projectmiga rerep_wf -o my_project
In the examples above, input genomes will be processed to evaluate quality, next they'll be classified, and finally they'll be dereplicated.