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
$ 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.