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Nextflow

Nextflow is being used by many bioinformatics researchers to develop scalable and reproducible scientific workflows using software containers (like Docker and Apptainer). See the Nextflow Quick Start here https://www.nextflow.io/index.html#GetStarted. Below we will follow the Quick Start guide.

Enter this command in your terminal: 

$ curl -s https://get.nextflow.io | bash

This will create a file nextflow in the current directory. 

$ curl -s https://get.nextflow.io | bash
CAPSULE: Downloading dependency org.multiverse:multiverse-core:pom:0.7.0
CAPSULE: Downloading dependency org.multiverse:multiverse:pom:0.7.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:pom:2.4.11
.......
CAPSULE: Downloading dependency com.amazonaws:aws-java-sdk-core:jar:1.11.172
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0

      N E X T F L O W
      version 0.26.1 build 4733
      last modified 17-11-2017 10:20 UTC (21:20 AEDT)
      cite doi:10.1038/nbt.3820
      https://nextflow.io

Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: /shared/homes/<your home>
- you may complete the installation by moving it to a directory in your $PATH
$

So that this executable will be in your path move it to your ~.bin/ directory.

$ mv nextflow bin/

Nextflow also requires a suitable Java version. You can load this with: 

$ module load java-latest

Now Nextflow should run without any errors. Note: You can unload this Java version with module unload java-latest.

You can get basic help for Nextflow like this:

$ nextflow help

and the current version:

$ nextflow -v
nextflow version 23.04.1.5866

Run the classic Hello world by entering the following command: 

$ nextflow run hello
N E X T F L O W  ~  version 0.26.1
Pulling nextflow-io/hello ...
 downloaded from https://github.com/nextflow-io/hello.git
Launching `nextflow-io/hello` [crazy_bartik] - revision: 1a373400ca [master]
[warm up] executor > local
[6e/7ab9be] Submitted process > sayHello (4)
[8b/7203d9] Submitted process > sayHello (1)
[f5/eeffe9] Submitted process > sayHello (2)
[9e/877afd] Submitted process > sayHello (3)
Bonjour world!
Ciao world!
Hello world!
Hola world!
$

Now that it is installed and running read the examples and documentation on the Nextflow site.