Plugins

Modified on Wed, 14 Sep 2022 at 05:59 AM

Q: Is it possible to use the Nextflow SQL DB plugin to query AWS Athena?

Yes. As of Nextflow 22.05.0-edge, your Nextflow pipelines can query data from AWS Athena. Add the following configuration items to your nextflow.config (Note: the use of secrets is optional):

plugins {
  id 'nf-sqldb@0.4.0'
}

sql {
    db {
        'athena' {
              url = 'jdbc:awsathena://AwsRegion=YOUR_REGION;S3OutputLocation=s3://YOUR_S3_BUCKET'
              user = secrets.ATHENA_USER
              password = secrets.ATHENA_PASSWORD
            }
    }
}

You can then call the functionality from within your workflow:

// Example
  channel.sql.fromQuery("select * from test", db: "athena", emitColumns:true).view()
}

For more information on the implementation, see this page.