Running the Pipeline

A Basic Example

Below is an example of how to run the pipeline setting only the most necessary parameters on an HPC.

nextflow run main.nf \
-profile sge,apptainer \
--inputdir path/input_directory_fastq \
--outputdir path/output_directory

Runtime Profiles

How you run the Nextflow pipeline depends on your environment (locally or on a cluster). Due to the large size of whole genome sequencing data, it is recommended to run the pipeline on a cluster like Wynton.

Runtime profiles will provide all dependencies and setup needed for different computing environments.

• 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.

The nextflow parameter -profile can be use to target the infrastructure you wish to run the pipeline on.

Apptainer (cluster)

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 (if it is not already built).

To build the image, run the command below from the conf directory:

apptainer build nf-wgs-dsl2.sif Apptainer

And then include the apptainer profile on the command line.

nextflow run main.nf \
-profile sge,apptainer \
--inputdir path/input_directory_fastq \
--outputdir path/output_directory

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 (local)

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.

Follow the steps below to setup your docker image from the conf directory:

Note: docker is a prerequisite.

docker build -t eppicenter/nf-wgs-dsl2 .

And you’re done! To run the pipeline, simply add -profile docker in your command.

nextflow run main.nf \
-profile docker \
--inputdir path/input_directory_fastq \
--outputdir path/output_directory

Conda (less recommended, under construction 🚧)

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 \
-profile conda \
--inputdir path/input_directory_fastq \
--outputdir path/output_directory