Hello World

Overview

  • Tutorial: 10 min

    Objectives:

    • Learn the how to write a minimal NextFlow workflow.

This Nextflow script defines a simple workflow that writes “Hello World!” to a file.

 1#!/usr/bin/env nextflow
 2
 3
 4process sayHello {
 5
 6    output:
 7        path 'output.txt'
 8
 9    script:
10    """
11    echo 'Hello World!' > output.txt
12    """
13}
14
15workflow {
16    sayHello()
17}

Process Block

A process in Nextflow is a unit of execution that runs independently. Here the process is called sayHello.

Output Directive

The output directive declares that this process produces an output file named output.txt. This file can be used as an input for other processes in a larger workflow.

Script Directive

The script directive defines defines the script that runs inside the process. This script writes “Hello World!” into output.txt.

Explanation

The script directive is enclosed in triple quotes (“”” or ‘’’) because it contains a multi-line shell script. This ensures that the script is correctly interpreted and formatted.

Workflow Block

The workflow block defines the execution order of processes. In this script it calls the sayHello process, executing it.

When you run Nextflow in a directory for the first time, it automatically creates a `work/` directory to store all generated files and symlinks during execution.

Inside the work/ directory, Nextflow organizes outputs and logs for each process call. For every execution of a process, it creates a uniquely named subdirectory (using a hash) where it: - Stages input files (linked via symlinks by default). - Stores helper files and execution logs. - Writes process output files.

The path to each process-specific subdirectory is displayed in truncated form within square brackets in the console output.

Key Points

  1. Process Block defines an independent execution unit (sayHello), which runs a script to generate an output file.

  2. Directives - The output directive specifies that output.txt is produced, while the script directive contains a shell script to write “Hello World!” into the file.

  3. Workflow Block determines execution order by calling sayHello(), triggering the process to run.

  4. Work Directory - Nextflow creates a work/ directory, organizing process outputs in uniquely named subdirectories, storing logs, inputs, and outputs.