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Linked all ingestion pipeline.yml files in parameter doc #173

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Feb 14, 2024
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Linked all ingestion pipeline.yml files in parameter doc #173

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Linked all ingestion pipeline.yml files in parameter doc.
Lilly-May Feb 13, 2024
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Lilly-May Feb 13, 2024
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11 changes: 11 additions & 0 deletions docs/yaml_docs/pipeline_ingestion_yml.md
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In this documentation, the parameters of the `ingest` configuration yaml file are explained.
This file is generated running `panpipes ingest config`. <br> The individual steps run by the pipeline are described in the [spatial preprocess workflow](../workflows/qc.md).

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.
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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)
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- `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)
- `pipeline.yml` file for [Ingesting multiome data from cellranger Tutorial](https://panpipes-tutorials.readthedocs.io/en/latest/ingesting_multiome/ingesting_mome.html): [Download here](https://github.com/DendrouLab/panpipes-tutorials/blob/main/docs/ingesting_multiome/pipeline.yml)


## Compute resources options

* <p class="parameter">resources</p>
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4 changes: 2 additions & 2 deletions panpipes/panpipes/pipeline_ingest/pipeline.yml
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# Ingest workflow Panpipes (pipeline_ingest.py)
# ============================================================
# This file contains the parameters for the ingest workflow.
# For full descriptions of the parameters, see the documentation at TODO
# For full descriptions of the parameters, see the documentation at https://panpipes-pipelines.readthedocs.io/en/latest/yaml_docs/pipeline_ingestion_yml.html


#--------------------------
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# RNA modality Quality Control

# Providing a gene list
# see documentation at https://panpipes-pipelines.readthedocs.io/en/latest/usage/gene_list_format.html#
# see documentation at https://panpipes-pipelines.readthedocs.io/en/latest/usage/gene_list_format.html
custom_genes_file: resources/qc_genelist_1.0.csv

# Defining actions on the genes
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