Metadata-Version: 2.1
Name: acanthophis
Version: 0.1.10
Summary: A comprehensive, opinionated plant variant calling pipeline in Snakemake
Home-page: https://github.com/kdm9/acanthophis
Author: Dr. K. D. Murray
Author-email: foss@kdmurray.id.au
License: UNKNOWN
Project-URL: Bug Tracker, https://github.com/kdm9/acanthophis/issues
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Unix Shell
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# Acanthophis

A reusable, comprehensive, opinionated plant variant calling pipeline in Snakemake

Until I write the documentation, please see [the example workflow](example/).
It should contain a fully working example workflow.

![Acanthophis, the most beautiful and badass of snakes](.github/logo.jpg)

## Installation & Use

```bash
# create conda env, activate it
conda create -n someproject python snakemake pip
conda activate someproject

# install acanthophis itself
pip install acanthophis

# generate boilerplate
acanthophis-init /path/to/someproject/

# edit config.yml to suit your project
vim config.yml

# run snakemake
snakemake -j 16 -p --use-conda --conda-frontend mamba --ri
# or on a cluster, see acanthophis-init --list-available-profiles
snakemake --profile ./ebio-cluster/
```


## About & Authors

This is an amalgamation of several pipelines developed between the [Weigel Group, MPI DB, Tübingen, DE](https://weigelworld.org), the [Warthmann Group, IAEA/FAO PBGL, Seibersdorf, AT](http://warthmann.com) and the [Borevitz Group, ANU, Canberra, AU](https://borevitzlab.anu.edu.au). This amalgamation authored by Dr. K. D. Murray, original code primary by K. D. Murray, Norman Warthmann, and Ilja Bezrukov, with contributions from others at the aforementioned institutes.


# TODO:

- [ ] break out more freebayes parameters to the config file
- [ ] merge sample bams before doing markdups


