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Lilly-May committed Feb 13, 2024
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Expand Up @@ -15,9 +15,9 @@ This file is generated running `panpipes ingest config`. <br> The individual st

When running the ingestion workflow, panpipes provides a basic `pipeline.yml` file.
To run the workflow on your own data, you need to specify the parameters described below in the `pipeline.yml` file to meet the requirements of your data.
However, we do provide pre-filled versions of the `pipeline.yml` file for individual tutorials.
However, we do provide pre-filled versions of the `pipeline.yml` file for individual [tutorials](https://panpipes-pipelines.readthedocs.io/en/latest/tutorials/index.html).
You can download the different ingestion pipeline.yml files here:
- Basic `pipeline.yml` file (not prefilled): [Download here](https://github.com/DendrouLab/panpipes/blob/main/panpipes/panpipes/pipeline_ingest/pipeline.yml)
- Basic `pipeline.yml` file (not prefilled) that is generated when calling `panpipes ingest config: [Download here](https://github.com/DendrouLab/panpipes/blob/main/panpipes/panpipes/pipeline_ingest/pipeline.yml)
- `pipeline.yml` file for [Ingesting data Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/ingesting_data/Ingesting_data_with_panpipes.html): [Download here](https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_data/pipeline.yml)
- `pipeline.yml` file for [Ingesting Mouse data Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/ingesting_mouse/Ingesting_mouse_data_with_panpipes.html): [Download here](https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_mouse/pipeline.yml)
- `pipeline.yml` file for [Ingesting multimodal (CITE-Seq + VDJ) data Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/ingesting_multimodal_data/ingesting_multimodal_data.html): [Download here](https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_multimodal_data/pipeline.yml)
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