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README_docker.md

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Build docker image

In folder where Dockerfile is located:

docker build -t pantools-qc-pipeline .

Run interactive container

Make sure you mount (-v "{folder-local-pc}:{folder-docker}") your configuration file and in- and output folders. Make sure the paths in your configuration file are pointing to the docker folder locations (/resources and /results in example)

docker run -v "/path/to/qc_config.yaml:/pantools-qc-pipeline/config/config.yaml" -v "/path/to/pantools-qc-pipeline/resources:/resources/" -v "/path/to/results:/results/" -it pantools-qc-pipeline bash

This creates an interactive container where you can run all snakemake commands as described in the README for the pipeline. Type exit when you want to stop the container.