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Preparing the Executor

Nextflow supports running pipelines on a variety of execution environments, including local machines, HPC systems, and cloud platforms. The default executor for this pipeline is SLURM, but you can easily switch between different environments by modifying the executor settings in the executor.config file.

Example: Setting LSF as the Executor​

To configure the pipeline to run with the LSF executor, update the process.executor as shown below:

config/executor.config
process{
    executor = 'slurm'
    memory = '28GB'
    time = '2d'
}

For running the pipeline with other supported executors such as PBS, k8s, AWS Batch,Google Cloud Batch that Nextflow currently supports, please refer to the Nextflow documentation for detailed instructions on configuring the desired execution environment.

Resource requirement:

  • Test Mode: The pipeline's test mode requires as little as 3G of memory, making it ideal for running on your local computer to validate the setup or debug issues.

  • Real Data Processing: When processing whole chromosomes with real data, you'll need at least 28G of memory. For such resource-intensive tasks, it is recommended to run the pipeline on an HPC or cloud system to ensure optimal performance.