# Part VI: Workflows

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

1. [Quality](/master/part6/quality_wf.md)
2. [Dereplicate](/master/part6/derep_wf.md)
3. [Classify](/master/part6/classify_wf.md)
4. [Preprocess](/master/part6/preproc_wf.md)
5. [Index](/master/part6/index_wf.md)

## 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.


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