Nextflow workflows for the analysis of samples using the megSAP pipeline.
The QBIC-megSAP-NGS pipeline is a medical genetics pipeline based on best-practices from imgag/megSAP and is primarily used for Exome analysis at our core-facility at QBIC, Germany.
The pipeline itself is developed at the Institute for Medical Genetics in Tuebingen, Germany. The accompanying scripts within this repository were however written for use at the QBIC and our local clusters CFC and BinAC.
The content of the megSAP/data folder is not bundled with this container to keep the actual pipeline separated from the data. In case you want to use this container on your own infrastructure, please download the data / tools yourself, index things using the scripts provided with the pipeline and then manually mount the paths to the respective data folder inside this container yourself.
Credits for the actual pipeline implementation should go to Marc Sturm and other contributors. See the respective repository for the development of the actual pipeline. The NextFlow pipeline and parts of this repository here have been implemented by Alex Peltzer (@apeltzer). Special thanks to Phil Ewels and Rickard Hammarén at SciLifeLab for providing templates, ideas and their own pipeline as a best-practice template for us when developing our own pipeline.
