Summary

This plugin implements a Nextflow executor for Hashicorp Nomad, enabling Nextflow pipelines to submit and manage tasks on Nomad clusters. It provides comprehensive support for Nomad-specific features including job configuration, resource allocation, constraints, secrets management, and distributed work directories for clusters without shared filesystems.

Get Started

To use this plugin in your Nextflow pipeline, add the following to your nextflow.config file:

plugins {
    id 'nf-nomad'
}

process {
    executor = 'nomad'
}

nomad {
    client {
        address = 'http://your-nomad-server:4646'
    }
}

Examples

The following example demonstrates how to configure a Nextflow pipeline to target a specific process to run on Nomad with customized datacenters and resource limits:

// nextflow.config
plugins {
  id 'nf-nomad'
}

process {
  executor = 'nomad'
  
  withName: runAlignment {
    nomadOptions = [
      datacenters: ['dc-analytics'],
      priority: 'high',
      resources: [
        cores: 8,
        memoryMax: '32 GB'
      ]
    ]
  }
}

Advanced process-level Nomad options:

process {
  withName: sayHello {
    nomadOptions = [
      datacenters: ['dc1', 'dc2'],
      namespace: 'bio',
      constraints: { node { unique = [name: params.RUN_IN_NODE] } },
      affinity: [attribute: '${meta.workload}', operator: '=', value: 'batch', weight: 25],
      meta: [owner: 'team-x', step: 'align'],
      shutdownDelay: '15s',
      failures: [
        restart: [attempts: 1, delay: '5s', mode: 'fail'],
        reschedule: [attempts: 2, delay: '10s']
      ],
      volumes: [[type: 'host', name: 'ref-data', path: '/ref', readOnly: true]],
      secretsPath: 'secret/projects/team-x',
      secrets: ['MY_ACCESS_KEY', 'MY_SECRET_KEY'],
      spread: [name: 'node.datacenter', weight: 50, targets: ['us-east1': 70, 'us-east2': 30]],
      priority: 'high',
      resources: [memoryMax: '64 GB', cores: 4, device: [[name: 'nvidia/gpu', count: 1]]]
    ]
  }
}

License

Apache License 2.0