> For the complete documentation index, see [llms.txt](https://manual.microbial-genomes.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://manual.microbial-genomes.org/part6.md).

# Part VI: Workflows

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

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