The Anthony Nichols Lab pipeline, including scripts to run WGS, WES, RNASeq, scRNAseq, and more

To run Compute Canada Niagara cluster, snakemake -s AN_WGS/Snakefile --cores 1 -j 40 --cluster "sbatch -N 1 -t 20:00:00 --ntasks 80 --output=logs/%x_%j.log" --ri

First, get access to the Niagara cluster and also BBUFFER

module load python/3.8.5
cd ~
virtualenv create -n snakemake7.20.0
source ~/snakemake7.20.0/bin/activate
pip install pulp==2.7.0 snakemake==7.20.0 pandas

Copy the profile config files to your ~/.config/snakemake/ and make them executable with chmod +x

Set the following paths in your ~/.bashrc

export NXF_SINGULARITY_CACHEDIR=/path/to/singularity/cache
export AN_WGS_temp=$BBUFFER
export SNAKEMAKE_OUTPUT_CACHE=$SCRATCH/temp
export REF_DIR=/path/to/reference/directory 

Commands for individual pipelines could be found in commands.txt

''' sudo mergerfs -o defaults,allow_other,use_ino,category.create=mfs,moveonenospc=true,minfreespace=1G /media/ionadmin/lab1:/media/ionadmin/lab2:/media/ionadmin/lab3:/media/ionadmin/lab4:/media/ionadmin/lab5:/media/ionadmin/lab6:/media/ionadmin/lab8:/media/ionadmin/lab9:/media/ionadmin/lab11:/media/ionadmin/lab13:/media/ionadmin/lab14:/media/ionadmin/lab15 /media/pool '''