Readme

Input to the pipeline:
1) Peaks folder consisting of all ATAC peaks bed file.
2) A consensus of all peaks bed file combined i.e. cat, merged and sorted.
3) Metadata file consisting of 4 columns rowsname "filename" "SampleName" "Group".

Install

1) git clone https://github.com/LupienLab/RepeatEnrichment.git
2) GO to RepeatEnrichment/config_slurm/   and pull singularity image
3) run -     singularity pull --arch amd64 library://nandankita/default/lupien-lab:ml_repeat_pipeline_v1.0 

To run the pipeline:

1) Snakemake is installed/loaded means run this command:   module load snakemake/5.20.1
2) Make sure you have all your input files.
3) Edit config.yaml to pass all correct variables.
4) from RepeatEnrichment directory run the command:   sbatch config_slurm/run-pipeline.sh

Singlarity is installed here on cluster:
h4h:
/cluster/tools/software/centos7/singularity/3.5.2/bin/singularity

mordor:
/mnt/work1/software/centos7/singularity/3.5.2/bin/singularity