CLI Workflows automate common tasks in MiGA. Currently implemented workflows include:

1. ​Quality​

2. ​Dereplicate​

3. ​Classify​

4. ​Preprocess​

5. ​Index​

Using multiple workflows

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_project
miga 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.