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Kafka plugin for Nextflow

This plugin provides an extension to implement built-in support for Kafka systems and manipulation in Nextflow scripts.

It provides the ability to create a Nextflow channel to listening from topics as send message.

The current version provides out-of-the-box support for the following systems:

NOTE: THIS IS A PREVIEW TECHNOLOGY, FEATURES AND CONFIGURATION SETTINGS CAN CHANGE IN FUTURE RELEASES.

Get started

Make sure to have Nextflow 22.10.0 or later. Add the following snippet to your nextflow.config file.

plugins {
  id '[email protected]'
}

Configuration

The plugin configuration is specified using the kafka scope:

Config option Description Mandatory
kafka.url The connection url. yes
kafka.group The group where the plugin will be attached. yes
kafka.pollTimeout The time that consumer will wait to consume from topic. no

For example:

kafka {
  url = 'localhost:902'
  group = 'group'
  pollTimeout = 2500 // ms
}

Available operations

This plugin adds to the Nextflow DSL the following extensions

fromTopic

The fromTopic factory method allows for performing a query against the topic specified and creating a Nextflow channel emitting a tuple for each record in the corresponding group with the key and value. For example:

include { fromTopic } from 'plugin/nf-kafka'

ch = channel.fromTopic('my-topic')

watchTopic

The watchTopic factory method allows to watch against the topic specified and creating a Nextflow channel emitting a tuple for each record in the corresponding group. For example:

include { watchTopic } from 'plugin/nf-kafka'

ch = channel.watchTopic('my-topic')
    .subscribe { println "new message received ${it[0]} = ${it[1]}" }
    .until{ it[1] == 'done' }

writeMessage

The writeMessage operator allows to send a message (with and optional key) to a topic

include { writeMessage; watchTopic } from 'plugin/nf-kafka'

process listener{
    input: val(msg)
    output: stdout 
    script:
        writeMessage('my-topic', 'Hi folks')                
        "echo ${msg[1]}"
}            
workflow{
    listener( Channel.of("msg") )
}

You need to provide the topic and the message plus an optional key

Develop

  1. build the plugin ./gradlew copyPluginZip

  2. create a docker-compose.yml and run docker-compose up -d to have a local instance running at localhost:29092

version: '2'
services:
  zookeeper:
    image: confluentinc/cp-zookeeper:latest
    environment:
      ZOOKEEPER_CLIENT_PORT: 2181
      ZOOKEEPER_TICK_TIME: 2000
    ports:
      - 22181:2181
  
  kafka:
    image: confluentinc/cp-kafka:latest
    depends_on:
      - zookeeper
    ports:
      - 29092:29092
    environment:
      KAFKA_BROKER_ID: 1
      KAFKA_ZOOKEEPER_CONNECT: zookeeper:2181
      KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,PLAINTEXT_HOST://localhost:29092
      KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: PLAINTEXT:PLAINTEXT,PLAINTEXT_HOST:PLAINTEXT
      KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT
      KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1
  1. create a Nextflow project and configure it
plugins{
   id '[email protected]'
}

kafka{    
    url='localhost:29092'
    group='group'
}

4.- create a run a listener pipeline

include { watchTopic } from 'plugin/nf-kafka'

process listener1{
    input: val(msg)
    output: stdout 
    script:       
    "echo '${msg[1]}'"
}            

workflow{    
        
    chn1 = channel.watchTopic("test").until{ it[1]=='done' }

    listener1(chn1) | view 

}

NXF_PLUGINS_DIR=//build/plugins/ nextflow run ./kafka-listener.nf

5.- create a run (in another shell) a producer

include { publishTopic } from 'plugin/nf-kafka'

workflow{    
        
    Channel.of(
        "Hi folks",
        "Another message",
        "done"
    ).publishTopic("test")

}

NXF_PLUGINS_DIR=//build/plugins/ nextflow run ./kafka-producer.nf

If all goes well, producer will send 3 messages to the topic and listener will print them and exit