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Groovy step

User-defined tasks can also be integrated by implementing a Groovy function. Compared to the Java Interface, there is no compilation needed and a script can be included directly.

Groovy provides a simple but rich IO API to read/write files or to execute external processes.


This step is currently under development and interfaces/methods can be changed in future releases.


Parameter Required Description
type yes Type has to be groovy
script yes The filename of your Groovy script (*.groovy)


Hello World

The following example demonstrates how to execute a Groovy script and write feedback to Cloudgene:


id: groovy-example
name: Groovy Example
version: 1.0
    - name: Execte Groovy step
      type: groovy
      script: step.groovy
    - id: name
      description: Name
      type: text
      value: World


Your Groovy script has to implement a method called run which can use the context to communicate with Cloudgene:

import genepi.hadoop.common.WorkflowContext

def run(WorkflowContext context) {

    // get input parameter 'name'
    def name = context.get("name");

    for (int i = 1; i <= 10; i++){
        // write to step output
        context.ok("Hello ${name}! I am Groovy Step Nr. " + i);

    return true;

Using external libraries

Cloudgene supports @Grab annotations to download missing dependencies automatically (e.g. from a Maven repository). The following example shows a Groovy script which parses a csv file using GroovyCSV:


import static com.xlson.groovycsv.CsvParser.parseCsv
import cloudgene.sdk.internal.WorkflowContext

def run(WorkflowContext context) {

    // get input parameter 'csv'
    def csvFilename = context.get('csv');

    def data = parseCsv(new FileReader(csvFilename), separator: '\t')
    for(line in data) {
        context.ok("$line.Name $line.Lastname")

    return true;

Learn more

Learn more about how to read/write files and execute external processes: