This pipeline will run QC measures of both genotype and phenotype data and will normalise quantified phenotypes.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

i. Install nextflow

ii. Install one of docker, singularity or conda

iii. Download the pipeline and test it on a minimal dataset with a single command

Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile institute in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

See usage docs for all of the available options when running the pipeline.

The eQTL-Catalogue/qcnorm pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

eQTL-Catalogue/qcnorm was originally written by Nurlan Kerimov.