App to simplify the celescope pipeline

Installation

Built with python 3.12

git clone https://github.com/edo98811/celescope-preprocessing.git
cd celescope-preprocessing
pip install .

or

pip install -e .

To install it as editable

Project Configuration

How to set up the settings configuration file. All paths are absolute

• GENOME_DIR: Specifies the directory containing genome files.

• DATA_DIR: Specifies the directory where raw data is located.

• OUTPUT_DIR: Specifies the directory where results will be saved.

• SAMPLE_LIST: Specifies a list of samples to be processed. Example: ["PD_021"]

Commands

• celescope-helper init-config requires one argument, path to the new config file that needs to be created, it needs to be a .json file Arguments: string, path to config file, including the name of the file, the name needs to be ajson file. example: "/mnt/S/edoardoStorage/config.json"

• celescope-helper tool preparegenome Only to be run once, to prepare the genome (and download it automatically from source).

• celescope-helper tool mapfile Create the mapfile.

• celescope-helper tool preparerun Run the celescope command to create the shell scripts necessary to run the pipeline.

• celescope-helper tool run Run celescope