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bio-la committed Apr 24, 2024
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19 changes: 17 additions & 2 deletions docs/yaml_docs/pipeline_refmap_yml.md
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Expand Up @@ -69,13 +69,28 @@ Specify one or more reference models to be used as reference. Users can also spe
Leave blank for no model specification.

- <span class="parameter">totalvi:</span> `String`, Default: path/to/totalvi<br>
Provide path to totalvi saved model.
Provide path to totalvi saved model. Multiple paths can be provided as a list:
```yaml
totalvi:
- path_to_totalvi1
- path_to_totalvi2

```
-

- <span class="parameter">impute_proteins</span> `Boolean`, Default: False<br>
- <span class="parameter">transform_batch</span> `String`, Default:<br>
Transform_batch is a batch-covariate specific to totalvi, allows the model to use the batch information in the query to mitigate
differences in protein sequencing depth.
- <span class="parameter">scvi</span> `String`, Default: path/to/scvi Mandatory, Provide a path to the scvi model. <br>
- <span class="parameter">scvi</span> `String`, Default: path/to/scvi Mandatory, Provide a path to the scvi model. Multiple paths can be provided as a list: <br>

```yaml
scvi:
- path_to_totalvi1
- path_to_totalvi2

```

- <span class="parameter">scanvi</span> `String`, Default:path/to/scanvi Mandatory, Provide a path to the scvi model.<br>
- <span class="parameter">run_randomforest</span> `Boolean`, Default:False<br>
Set to true if the reference model has a trained random forest classifier to transfer the labels.
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