{"id":15899531,"url":"https://github.com/adonath/snakemake-workflow-chandra","last_synced_at":"2026-02-02T05:33:27.069Z","repository":{"id":68491713,"uuid":"602190503","full_name":"adonath/snakemake-workflow-chandra","owner":"adonath","description":"A Snakemake workflow for Chandra data reduction","archived":false,"fork":false,"pushed_at":"2025-08-12T14:28:53.000Z","size":553,"stargazers_count":2,"open_issues_count":2,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-09-09T00:08:05.418Z","etag":null,"topics":["chandra","ciao","data-reduction","jolideco","pylira","snakemake"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/adonath.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-02-15T17:28:53.000Z","updated_at":"2025-09-05T21:17:39.000Z","dependencies_parsed_at":"2023-12-31T00:13:16.931Z","dependency_job_id":"ffc9f8a2-a40e-4ec6-a448-58167afb74cb","html_url":"https://github.com/adonath/snakemake-workflow-chandra","commit_stats":{"total_commits":62,"total_committers":3,"mean_commits":"20.666666666666668","dds":"0.19354838709677424","last_synced_commit":"cd457c0fb338f70870aedeafd6eb6034f219f99f"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/adonath/snakemake-workflow-chandra","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adonath%2Fsnakemake-workflow-chandra","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adonath%2Fsnakemake-workflow-chandra/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adonath%2Fsnakemake-workflow-chandra/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adonath%2Fsnakemake-workflow-chandra/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/adonath","download_url":"https://codeload.github.com/adonath/snakemake-workflow-chandra/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/adonath%2Fsnakemake-workflow-chandra/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":284893575,"owners_count":27080531,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-11-17T02:00:06.431Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["chandra","ciao","data-reduction","jolideco","pylira","snakemake"],"created_at":"2024-10-06T10:21:41.729Z","updated_at":"2025-11-17T13:57:11.285Z","avatar_url":"https://github.com/adonath.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![DOI](https://zenodo.org/badge/602190503.svg)](https://doi.org/10.5281/zenodo.16813370)\n\n# Snakemake Workflow for Chandra Data Reduction\n\nThis is an example snakemake workflow for data reduction of Chandra data. \nThe workflow will run the standrad `ciao` tools for a given configuration\nand produce as output FITS files. Thereby it will handle the reduction of\n counts, exposure and point spread function (PSF).\n\n## Getting Started\n### Use as Snakemake Module (recommended)\n\nIf you would like use this as Snakmake module you should add e.g. the following to your `Snakefile`:\n\n```python3\nmodule chandra_data_workflow:\n    snakefile:\n        # here, plain paths, URLs and the special markers for code hosting providers (see below) are possible.\n        github(\"adonath/snakemake-workflow-chandra\", path=\"workflow/Snakefile\", branch=\"main\")\n    config: config[\"chandra-data\"]\n\nuse rule * from chandra_data_workflow as chandra_data_*\n```\n\nSee also https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modularization\n\n### Setup Environment \nStart by cloning this repository to your local machine:\n```bash\ngit clone https://github.com/adonath/snakemake-workflow-chandra.git\n```\n\nIf you havn't done yet, please install [conda](https://www.anaconda.com/products/distribution)\nor [mamba](https://mamba.readthedocs.io/en/latest/installation.html).\n\nNow change to the directory of the repository:\n```bash\ncd snakemake-workflow-chandra/\n```\n\nAnd create the conda environment using:\n```bash\nmamba env create -f environment.yaml\n```\n\nOnce the process is done you can activate the environment:\n\n```bash\nconda activate snakemake-workflow-chandra\n```\n\n### Configure and Run the Workflow\nNow you should adapt the configuration in [config/config.yaml](config/config.yaml)\nto match your data. \n\nThen you are ready to run the workflow, like:\n```bash\nsnakemake --cores 8 --use-conda --configfile config/config.yaml\n```\n\nYou can also create a report to see previews of the counts, exposure and PSF images:\n```bash\nsnakemake --report report.html\nopen report.html\n```\n\nYou can also create a directed acyclic graph (DAG) visualization of the workflow:\n\n```bash\nsnakemake --dag | dot -Tpng \u003e dag.png\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadonath%2Fsnakemake-workflow-chandra","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fadonath%2Fsnakemake-workflow-chandra","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fadonath%2Fsnakemake-workflow-chandra/lists"}