This nextflow pipeline is designed to generate the RADlib databases used in the RADlib suite.
Currently, this pipeline is only available on GitHub.
To clone this repository, run
git clone --recurse-submodules https://github.com/RADSuite/RADLibCreator.git
This workflow is written for Nextflow 25. If you have nextflow installed, make sure it is at least version 25. If you do not have nextflow installed, you can see if your system meets the requirments to run Nextflow here To download Nextflow, you can follow the instructions here. Nextflow can be installed without Conda but it is recommended.
It is recommended that you use a container such as Docker or Singularity/Apptainer to run this workflow. It is possible to create a Conda environment and use that to run the workflow but it is prone to incompatability issues
Start by downloading Docker. Docker provides instructions on how to download the version of Docker for your OS and archetecture here. It is recommended to download Docker desktop if you are not use to running docker in the terminal.
Once Docker is installed, you can build the RADlib Docker container by running
docker build -t radlib:latest container-files
This docker container is 4.22GB so make sure you have enough available storage.
Docker is not available on most HPC so an Apptainer/Singularity .def file is also available in the container-files directory. You can run this command to create the Apptainer image.
apptainer build my_image.sif
It is not recommended to just use Conda but if you do not have access to container programms a conda enviroment can be created. A Conda yaml file is provided in the container-files directory to create an environment.
conda env create -f container-files/rad_nextflow_conda.yml
This workflow creates a large number of files so please be cautious of the limits your device has: memory, storage, and any file number limits.
To try the workflow on a local device, you can run
nextflow run workflows/rad_workflow.nf -profile test,docker
To run the full workflow, run
nextflow run workflows/rad_workflow.nf -profile docker
If you are not using Docker, replace the
dockerparameter withapptainerorconda.
If you run into issues with the number of files created during exicutions, each subworkflow can be run independently. Follow these steps to run each step.
nextflow run workflows/download_ncbi_genes/download_ncbi_data.nf -profile docker
nextflow run workflows/extract_16s_genes/extract_16s_genes.nf -profile docker
nextflow run workflows/create_radlib_16s/create_radlib_16s.nf -profile docker
nextflow run workflows/create_radlib_vr/create_radlib_vr.nf -profile docker
In future itterations of the RADlibCreate pipeling, we hope to remove the dependency on annotated wgs from ncbi so users can create RADlibs with their own data.
We also hope to publish this workflow to nf-core and the Docker image to Dockerhub.