Nf-amazon Plugin Missing In Nextflow 25.10.0: How To Fix?

Experiencing issues with the nf-amazon plugin in Nextflow version 25.10.0? You're not alone. This article dives into a common problem where Nextflow fails to recognize the nf-amazon plugin when attempting to read parameter files directly from an Amazon S3 bucket. We'll explore the bug report, understand the cause, and provide solutions to get your Nextflow pipelines running smoothly again.

Understanding the Issue

The core problem lies in the fact that Nextflow version 25.10.0 seems to have a hiccup when it comes to automatically loading the nf-amazon plugin, which is essential for interacting with S3. When you specify an S3 path for your -params-file, Nextflow should use this plugin to retrieve the configuration. However, in this specific version, it throws an error indicating the plugin is missing, even though it's expected to be handled seamlessly.

The user's bug report highlights this clearly:

• Using Nextflow version 25.10.0.
• Attempting to run a Nextflow pipeline with a -params-file located on S3 (e.g., s3://example_bucket/hello/params.json).
• Encountering the error: Missing plugin 'nf-amazon' required to read file.
• The issue does not occur in Nextflow version 25.04.8, where the S3 path is correctly accessed (though a different error might arise if the path doesn't exist, which is a separate, valid issue).

This behavior suggests a regression in how Nextflow 25.10.0 handles the nf-amazon plugin, specifically regarding its automatic loading when encountering S3 paths. The subsequent sections will guide you on how to address this and get your pipelines working again.

Steps to Reproduce the Problem

To replicate the issue, follow these simple steps:

1. Ensure you have Nextflow version 25.10.0 installed.

2. Prepare a params.json file and upload it to an S3 bucket. You can use a basic JSON structure for testing purposes.

3. Run a Nextflow pipeline, specifying the S3 path to your params.json file using the -params-file option:

   nextflow run https://github.com/seqeralabs/nf-hello-world -params-file s3://your_bucket_name/path/to/params.json
   

   Replace your_bucket_name and path/to/params.json with your actual S3 bucket and file path.

4. Observe the error message indicating the missing nf-amazon plugin.

This straightforward reproduction confirms the bug and sets the stage for implementing the solutions outlined below.

Possible Solutions to the nf-amazon Plugin Issue

Several approaches can mitigate the nf-amazon plugin problem in Nextflow 25.10.0.

1. Explicitly Declare the Plugin in your nextflow.config

One of the most reliable solutions is to explicitly declare the nf-amazon plugin in your nextflow.config file. This ensures that Nextflow loads the plugin before attempting to access the S3 resource. By explicitly declaring the plugin, you ensure that Nextflow recognizes and loads it before attempting to access any S3 resources. To explicitly declare the nf-amazon plugin, you need to modify your nextflow.config file. If you don't have one, create a file named nextflow.config in your pipeline directory. Add the following lines to your nextflow.config file:

plugins {
    amazon = 'nf-amazon'
}

This configuration tells Nextflow to load the nf-amazon plugin at the start of the execution. After adding this configuration, rerun your Nextflow pipeline with the S3 -params-file. This should resolve the issue by ensuring that the nf-amazon plugin is properly loaded and available when Nextflow attempts to read the parameter file from S3. This method is generally the most recommended as it directly addresses the plugin loading issue.

2. Downgrade Nextflow Version

As the bug report indicates, the issue is specific to version 25.10.0. Downgrading to a previous version, such as 25.04.8, where the nf-amazon plugin works correctly, is a viable workaround. While this is a workaround rather than a direct fix, downgrading can quickly restore functionality if you're facing immediate deadlines or need to maintain pipeline stability. To downgrade, use the following command:

nxf self-update 25.04.8

After downgrading, rerun your pipeline with the S3 -params-file. The nf-amazon plugin should now be loaded correctly, allowing Nextflow to access the parameter file from S3. Keep in mind that downgrading might mean missing out on newer features or bug fixes present in version 25.10.0, so evaluate whether this trade-off is acceptable for your specific use case.

3. Use a Script to Download the params-file

Instead of directly specifying the S3 path in the nextflow run command, you can use a script to download the params-file from S3 to your local file system before running the pipeline. This involves creating a simple script that uses AWS CLI or another tool to download the file. This approach bypasses the need for Nextflow to directly interact with S3 for the -params-file, thus avoiding the plugin loading issue. Here's how you can implement this workaround:

1. Create a Download Script: You can use the AWS CLI, which is a command-line tool for interacting with AWS services. If you don't have it installed, you can install it using pip: pip install awscli. Configure the AWS CLI with your credentials using aws configure. Create a script (e.g., download_params.sh) with the following content:

   #!/bin/bash
   aws s3 cp s3://your_bucket_name/path/to/params.json params.json
   

   Replace your_bucket_name and path/to/params.json with your actual S3 bucket and file path. Make the script executable:

   chmod +x download_params.sh
   

2. Run the Script Before Nextflow: Before running your Nextflow pipeline, execute the download script:

   ./download_params.sh
   

   This will download the params.json file from S3 to your current directory.

3. Run Nextflow with the Local File: Now, run your Nextflow pipeline, specifying the local path to the params.json file:

   nextflow run https://github.com/seqeralabs/nf-hello-world -params-file params.json
   

   Since the params.json file is now local, Nextflow doesn't need to use the nf-amazon plugin to access it, thus avoiding the error. This method is particularly useful if you want to ensure that the parameter file is always available locally before running the pipeline or if you have other reasons to avoid direct S3 access from Nextflow.

Conclusion

The nf-amazon plugin issue in Nextflow 25.10.0 can be a stumbling block when working with S3-based parameter files. By explicitly declaring the plugin in your nextflow.config, downgrading to a previous version, or using a script to download the params-file locally, you can effectively work around this problem. Remember to choose the solution that best fits your specific needs and infrastructure. Always keep an eye on Nextflow release notes for official bug fixes and updates. For more information about Nextflow plugins, you can check the official documentation on the Nextflow website.