1. Orientation¶

The Gitpod environment contains some test data that will be used in this workshop.

Note

Follow this link if you have not yet setup your Gitpod environment.

1.1 Getting started¶

You will complete this module in the nf-training-advanced/ folder.

In this folder you will find a series of folders that will be used during different sections of this training.

nf-training-advanced
├── groovy
│   ├── main.nf
│   ├── modules
│   │   └── local
│   │       └── fastp
│   │           └── main.nf
│   └── nextflow.config
├── grouping
│   ├── data
│   │   ├── genome.fasta
│   │   ├── genome.fasta.fai
│   │   ├── intervals.bed
│   │   ├── reads
│   │   │   ├── treatmentA
│   │   │   │   └── <data files>
│   │   │   └── treatmentB
│   │   │       └── <data files>
│   │   ├── samplesheet.csv
│   │   └── samplesheet.ugly.csv
│   └── main.nf
├── metadata
│   ├── data
│   │   ├── reads
│   │   │   ├── treatmentA
│   │   │   │   └── <data files>
│   │   │   └── treatmentB
│   │   │       └── <data files>
│   │   ├── samplesheet.csv
│   │   └── samplesheet.ugly.csv
│   └── main.nf
├── operators
│   ├── data
│   │   ├── reads
│   │   │   └── <data files>
│   │   ├── samplesheet.csv
│   │   └── samplesheet.ugly.csv
│   └── main.nf
└── structure
    ├── lib
    │   └── Food.groovy
    ├── main.nf
    └── templates
        ├── adder.py
        └── demo_script.sh

1.2 Selecting a Nextflow version¶

By default, Nextflow will pull the latest stable version into your environment.

However, Nextflow is constantly evolving as we make improvements and fix bugs.

The latest releases can be viewed on GitHub here.

If you want to use a specific version of Nextflow, you can set the NXF_VER variable as shown below:

export NXF_VER=23.10.0

Note

This tutorial workshop requires NXF_VER=23.10.0, or later.

Run nextflow -version again to confirm that the change has taken effect.