acanthophis 0.1.10

A comprehensive, opinionated plant variant calling pipeline in Snakemake

Acanthophis

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

Until I write the documentation, please see the example workflow. It should contain a fully working example workflow.

Installation & Use

# 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, the Warthmann Group, IAEA/FAO PBGL, Seibersdorf, AT and the Borevitz Group, ANU, Canberra, 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