conda-snakemake-gatk

snakemake pipeline for gatk running on binder

initialize index and dictionary

If you clone this repo, index and dictionary are already included. If you use different genome or change location of genome please run initialize rule first

snakemake --use-conda -s rules/initialize.smk 

local use

snakemake  --use-conda --cores 8

after pipeline finishes, you can generate the report with following command

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

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 in your TRUBA home directory

. "/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:

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