Getting Started

The mad4hatter pipeline uses nextflow and will need to be installed prior to using the pipeline. Information about how to install and use the command line tool can be found on their website. The tool is also available from other package managers such as conda if you would like an alternative installation pathway.

Nextflow requires the Java 11 (or higher) Runtime Environment.

Runtime Profiles

Runtime profiles will provide all dependencies and setup needed for different computing environments. As an example, if you are using a cluster, grid or HPC environment, apptainer would be an appropriate profile as it supplies an image with all dependencies ready. If you are using a local computer, docker would be more appropriate. You can also choose to install the dependencies independently and run the pipeline that way if you choose to, but it is not recommended.

Currently, Sun of Grid Engine (SGE) is the only supported cluster environment.

Apptainer

Apptainer is a prerequisite.

Apptainer should be used if you are using a computing cluster or grid. You will first need to build the apptainer image before you can use the image.

To build the image, run the command below:

apptainer build mad4hatter.sif Apptainer

And then include the apptainer profile on the command line.

nextflow run main.nf --readDIR /wynton/scratch/data/AAD1017 --target v4 -profile sge,apptainer -c conf/custom.config

You should also include the job scheduler you will be using. In this case, sge is the job scheduler that will be used. Contact your system administrator if you are unsure about this setting.

Docker

Docker is a prerequisite.

The pipeline can be easily run with docker and is the recommended way to run it when not using an HPC.

The EPPIcenter has a repository for images, and the docker image for the pipeline will be automatically pulled in the background when first running the pipeline. The image will then be stored locally on your machine and reused.

To run the with docker, simply add -profile docker in your command.

nextflow run main.nf --readDIR /wynton/scratch/data/AAD1017 --outDIR /wynton/scratch/results -profile docker --genome /wynton/share/PlasmoDB-59_Pfalciparum3D7_Genome.fasta --target v4 -config conf/custom.config

Alternatively, you can build the docker image on your machine using the Dockerfile recipe, although this is not the recommended way to set up the docker image.

If you would like to build the docker image yourself, you may run the command below:

docker build -t eppicenter/mad4hatter:latest .

Conda

To use conda, you must first install either conda or miniconda. Once installed, include the conda profile on the command line.

nextflow run main.nf --readDIR /wynton/scratch/data --outDIR /wynton/scratch/results -profile conda --genome /wynton/share/PlasmoDB-59_Pfalciparum3D7_Genome.fasta --target v4 -config conf/custom.config