# Part VI: Workflows

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

1. [Quality](https://manual.microbial-genomes.org/master/part6/quality_wf)
2. [Dereplicate](https://manual.microbial-genomes.org/master/part6/derep_wf)
3. [Classify](https://manual.microbial-genomes.org/master/part6/classify_wf)
4. [Preprocess](https://manual.microbial-genomes.org/master/part6/preproc_wf)
5. [Index](https://manual.microbial-genomes.org/master/part6/index_wf)

## 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:

```bash
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:

```bash
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.