diff --git a/docs/yaml_docs/pipeline_ingestion_yml.md b/docs/yaml_docs/pipeline_ingestion_yml.md index c1ebed3a..5efe79d2 100644 --- a/docs/yaml_docs/pipeline_ingestion_yml.md +++ b/docs/yaml_docs/pipeline_ingestion_yml.md @@ -13,6 +13,17 @@ In this documentation, the parameters of the `ingest` configuration yaml file are explained. This file is generated running `panpipes ingest config`.
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. +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) +- `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 *

resources

diff --git a/panpipes/panpipes/pipeline_ingest/pipeline.yml b/panpipes/panpipes/pipeline_ingest/pipeline.yml index ded81dba..83763ac8 100644 --- a/panpipes/panpipes/pipeline_ingest/pipeline.yml +++ b/panpipes/panpipes/pipeline_ingest/pipeline.yml @@ -2,7 +2,7 @@ # 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 #-------------------------- @@ -79,7 +79,7 @@ scr: # 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