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snakemake-vcfcalling_ozy's Introduction

Binder

conda-snakemake-gatk

snakemake pipeline for gatk running on binder

local use

snakemake  --use-conda --cores 8

cluster instructions

after installing conda in the cluster, edit the truba.json file and then please run following commands

git clone https://github.com/alperyilmaz/conda-snakemake-gatk/

cd conda-snakemake-gatk/

conda install pandas jinja2 networkx pygraphviz

snakemake -j 999 --use-conda --cluster-config truba.json --cluster "sbatch -A {cluster.account} -p {cluster.partition} -n {cluster.n}  -t {cluster.time} --constraint {cluster.constraint} --export=PATH"

snakemake --use-conda --report gatk-report.html

please make sure your .bashrc file contains the following lines

. "/truba/home/USERNAME/miniconda3/etc/profile.d/conda.sh"
export PATH="/truba/home/USERNAME/miniconda3/bin:$PATH"

you might need to comment out conda initialize section in .bashrc

The pipeline will run the following rules in order:

dag-rules

Speficic for this test, following DAG will be executed for given samples and units.

whole-dag

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