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https://github.com/kdm9/acanthophis
A comprehensive, opinionated plant metagenomics and variant calling pipeline in Snakemake
https://github.com/kdm9/acanthophis
Last synced: 11 days ago
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A comprehensive, opinionated plant metagenomics and variant calling pipeline in Snakemake
- Host: GitHub
- URL: https://github.com/kdm9/acanthophis
- Owner: kdm9
- License: mpl-2.0
- Created: 2021-03-08T01:30:24.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-08-26T10:45:24.000Z (3 months ago)
- Last Synced: 2024-10-11T19:22:41.608Z (about 1 month ago)
- Language: TeX
- Homepage:
- Size: 617 KB
- Stars: 8
- Watchers: 1
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
# Acanthophis
[](https://doi.org/10.21105/joss.06062)
A reusable, comprehensive, opinionated Snakemake pipeline for plant-microbe genomics and plant variant calling.
# Documentation
For documentation, see [./documentation.md](documentation.md). In summary:
```bash
# create conda env, activate it
mamba create -n someproject python snakemake pip natsort
mamba activate someproject
# Install acanthophis itself
pip install acanthophis
# Generate a workspace. This copies all files the workflow will need to your
# workspace directory.
acanthophis-init /path/to/someproject/
# Edit config.yml to suit your project. Hopefully this config file documents
# all options available in an understandable fashion. If not, please raise an
# issue on github.
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/
```
### Compatibility
While snakemake and Acanthophis are cross-platform, most of the underlying tools are only packaged for and/or only operate on Linux `x68_64`. Therefore, I only support users on Linux systems. In theory, everything *should* run on OSX or WSL, but the vast majority of users will want to utilise a high performance linux workstation (at least, probably more likely a cluster).
### Running tests
For running tests, see [./tests/README.md](tests/README.md).
# Contribution & Assistance
If you have anything (advice, docs, code) you'd like to contribute, pull requests are more than welcome. Please discuss any major contribution in a new issue before implementing it, to avoid wasted effort.
If you need any assistance, or have other questions or comments, please make an issue on github, or open a discussion. Unfortunately both need an account on github, so alternatively you can email me (`foss kdmurray.id.au`).
## 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,
with contributions from others at the aforementioned institutes.