2  Running Nextflow Pipelines from GitHub Repositories

Follow these steps to run Nextflow pipelines hosted on GitHub:

Prerequisites

• Nextflow: Ensure Nextflow is installed on your system. Follow the official installation guide.
• Docker: Many Nextflow pipelines require Docker. Install Docker by following the official guide.

1. Prepare Your Environment

Ensure your Nextflow and Docker installations are up to date and correctly configured.

2. Define the Pipeline Repository

Define the GitHub repository and its version containing the Nextflow pipeline you wish to run:

nextflowScript = <Repository_URL>
nextflowScriptVersion = <Repository_Version>'
# Replace <Repository_URL> and <Repository_Version> with the appropriate values for the pipeline you're using.

3. Configure Pipeline Parameters

Identify the input parameters required by the pipeline. These may include paths to input files, output directories, and other configuration options. Set these parameters using variables:

input="path/to/input"
outputPath="path/to/output"
# Add more variables as needed

4. Run the Pipeline

Construct and execute the Nextflow command with your parameters:

nextflow run  ${nextflowScript} -r ${nextflowScriptVersion} -with-docker --input '${input}' --output '${outputPath}' # Add other parameters as needed
#Replace --input and --output with the appropriate parameter names for your pipeline.

5. Monitor Execution and Check Outputs

Nextflow will print progress logs to the console. Monitor these logs to ensure the pipeline is executing as expected. Outputs will be saved to the specified output directory.

By following these steps, you can run any Nextflow pipeline hosted on GitHub. Customize the input parameters and execution options based on the specific requirements of the pipeline you’re using.