GwasQcPipeline

QC pipeline for Illumina SNP Array data generated at CGR.

Usage

If you use this workflow in a paper, please cite the URL of this repository (https://github.com/NCI-CGR/GwasQcPipeline).

The documentation of this pipeline is at https://nci-cgr.github.io/GwasQcPipeline/

Deploying with Docker

Build docker image from within GwasQcPipeline directory

docker build -t gwas_qc_pipe .

Test docker image if you have test data

docker run -v $(pwd):/home/data -i -t gwas_qc_pipe snakemake -k --use-conda -npr

Installing GwasQcPipeline on ccad2

• Install miniconda and then create GwasQcPipeline production environment

  $ mkdir /scratch/myfolder/GwasQcPipeline_v1.4.0
  $ cd /scratch/myfolder/GwasQcPipeline_v1.4.0
  $ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
  $ bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /scratch/myfolder/GwasQcPipeline_v1.4.0/conda -b
  $ source conda/bin/activate base
  (base) $ conda update -n base -c defaults conda
  (base) $ conda install -n base -c conda-forge mamba
  (base) $ conda create -n GwasQcPipeline -y python=3.8 pip
  (base) $ conda deactivate

• Install GwasQcPipeline source code

  $ source /scratch/myfolder/GwasQcPipeline_v1.4.0/conda/bin/activate GwasQcPipeline
  (GwasQcPipeline) $ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.4.0/cgr_gwas_qc-1.4.0-py3-none-any.whl
  (GwasQcPipeline) $ cgr --help
  (GwasQcPipeline) $ cgr version
  v1.4.0

  Usage

  cgr submit --ccad2 --local-mem-mb 8000