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https://github.com/adonath/snakemake-workflow-chandra

A Snakemake workflow for Chandra data reduction

https://github.com/adonath/snakemake-workflow-chandra

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
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    Institutional organization owner
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    Scientific vocabulary similarity
    Low similarity (12.8%) to scientific vocabulary

Keywords

chandra ciao data-reduction pylira snakemake
Last synced: 6 months ago · JSON representation

Repository

A Snakemake workflow for Chandra data reduction

Basic Info
  • Host: GitHub
  • Owner: adonath
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 538 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Topics
chandra ciao data-reduction pylira snakemake
Created about 3 years ago · Last pushed 9 months ago
Metadata Files
Readme License

README.md

DOI

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 chandradataworkflow: 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 chandradataworkflow as chandradata* ```

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 or mamba.

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 to match your data.

Then you are ready to run the workflow, like: bash snakemake --cores 8 --use-conda --configfile config/config.yaml

You can also create a report to see previews of the counts, exposure and PSF images: bash snakemake --report report.html open report.html

You can also create a directed acyclic graph (DAG) visualization of the workflow:

bash snakemake --dag | dot -Tpng > dag.png

Owner

  • Name: Axel Donath
  • Login: adonath
  • Kind: user
  • Location: Cambridge, MA
  • Company: Center for Astrophysics | Havard & Smithonian

I'm a Postdoc researcher at Center for Astrophysics. I work on statistical methods for analysis of low counts astronomical data.

GitHub Events

Total
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 8
  • Fork event: 2
Last Year
  • Issues event: 2
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 8
  • Fork event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 62
  • Total Committers: 3
  • Avg Commits per committer: 20.667
  • Development Distribution Score (DDS): 0.194
Past Year
  • Commits: 62
  • Committers: 3
  • Avg Commits per committer: 20.667
  • Development Distribution Score (DDS): 0.194
Top Committers
Name Email Commits
Axel Donath a****h@c****u 50
Axel Donath a****h 11
Axel Donath a****h@m****e 1
Committer Domains (Top 20 + Academic)
mpi-hd.mpg.de: 1 cfa.harvard.edu: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adonath (1)
  • zknutson (1)
  • DougBurke (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

environment.yaml pypi
.github/workflows/ci_test.yaml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • conda-incubator/setup-miniconda v2 composite