Part VI: Workflows

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.