UMI Injector

umi-injector integrates UMI sequences from a separate FastQ file into the read headers of a single or paired FastQ.

Building the containerized versions

Building locally

To build the image locally, Docker (e.g. Docker Desktop) needs to be installed on your system. You can build the CPU version of the image directly off this Git repository. Specify a tag name with the -t parameter.

docker build https://github.com/NationalGenomicsInfrastructure/umi-injector.git -t umi-injector

Alternatively, you can also clone this repository beforehand

git clone https://github.com/NationalGenomicsInfrastructure/umi-injector.git && cd umi-injector
docker build . --file Dockerfile -t umi-injector

Building on Github Actions

This repository also contains a Github Action workflow to build the container image.

To run the workflow successfully, you need to fork the repository and create your own repository secrets. Navigate to Settings and then to Secrets, where you need to create the two secrets DOCKERHUB_USERNAME and DOCKERHUB_TOKEN. Both will be needed by the workflow to upload the finished container image to Docker Hub.

The workflow can be dispatched manually in the Actions tab. Choose the desired settings in the dialogue and launch the workflow run.

Running containerized umi-injector

To run the containerized version of umi-injector, invoke the container like so

docker run --rm -itv $(pwd):$(pwd) -w $(pwd) umi-injector

Replace umi-injector with whatever tag you specified to the -t parameter when building the container image.

To simplify the invocation, you can also declare an alias, which can be perpetuated in your ~/.bashrc respectively ~/.zshrc.

alias umi-injector="docker run --rm -itv $(pwd):$(pwd) -w $(pwd) umi-injector"

License