https://github.com/adonath/snakemake-workflow-chandra
A Snakemake workflow for Chandra data reduction
https://github.com/adonath/snakemake-workflow-chandra
chandra ciao data-reduction pylira snakemake
Last synced: about 1 month ago
JSON representation
A Snakemake workflow for Chandra data reduction
- Host: GitHub
- URL: https://github.com/adonath/snakemake-workflow-chandra
- Owner: adonath
- License: other
- Created: 2023-02-15T17:28:53.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-07-30T20:58:13.000Z (10 months ago)
- Last Synced: 2025-03-17T21:39:46.422Z (2 months ago)
- Topics: chandra, ciao, data-reduction, pylira, snakemake
- Language: Python
- Homepage:
- Size: 518 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# Snakemake Workflow for Chandra Data Reduction
This is an example snakemake workflow for data reduction of Chandra data.
The workflow will run the standrad `ciao` tools for a given configuration
and produce as output FITS files. Thereby it will handle the reduction of
counts, exposure and point spread function (PSF).
## Getting Started
### Use as Snakemake Module (recommended)
If you would like use this as Snakmake module you should add e.g. the following to your `Snakefile`:
```python3
module chandra_data_workflow:
snakefile:
# here, plain paths, URLs and the special markers for code hosting providers (see below) are possible.
github("adonath/snakemake-workflow-chandra", path="workflow/Snakefile", branch="main")
config: config["chandra-data"]
use rule * from chandra_data_workflow as chandra_data_*
```
See also https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modularization
### Setup Environment
Start by cloning this repository to your local machine:
```bash
git clone https://github.com/adonath/snakemake-workflow-chandra.git
```
If you havn't done yet, please install [conda](https://www.anaconda.com/products/distribution)
or [mamba](https://mamba.readthedocs.io/en/latest/installation.html).
Now change to the directory of the repository:
```bash
cd snakemake-workflow-chandra/
```
And create the conda environment using:
```bash
mamba env create -f environment.yaml
```
Once the process is done you can activate the environment:
```bash
conda activate snakemake-workflow-chandra
```
### Configure and Run the Workflow
Now you should adapt the configuration in [config/config.yaml](config/config.yaml)
to match your data.
Then you are ready to run the workflow, like:
```bash
snakemake --cores 8
```
You can also create a report to see previews of the counts, exposure and PSF images:
```bash
snakemake --report report.html
open report.html
```