Orientation

Tour of Gitpod

If you haven't yet, log into the , which provides a virtual machine with everything already set up for you.

In the Gitpod window, you'll see a terminal. Type the following command to switch to the folder of this training material:

cd /workspace/gitpod/hello-nextflow

Take a few minutes to familiarize yourself with the gitpod environment, especially the file explorer, file browser and terminal.

Pipeline data and scripts

We provide all test data, code and accessory needed to work through this training module. To view a full list, run the following command in the Gitpod terminal:

tree /workspace/gitpod/hello-nextflow

You should see the following output:

Output

hello-nextflow
├── data
│   ├── bam
│       ├── reads_father.bam
│       ├── reads_mother.bam
│       └── reads_son.bam
│   ├── intervals.list
│   ├── ref.tar.gz
│   ├── sample_bams.txt
│   └── samplesheet.csv
├── scripts
│   ├── hello-gatk-1.nf
│   ├── hello-gatk-2.nf
│   ├── hello-gatk-3.nf
│   ├── hello-gatk-4.nf
│   ├── hello-gatk-5.nf
│   ├── hello-gatk-6.nf
│   ├── hello-world-1.nf
│   ├── hello-world-2.nf
│   ├── hello-world-3.nf
│   ├── hello-world-4.nf
│   ├── hello-world-5.nf
│   ├── hello-world-6.nf
│   ├── hello-world-7.nf
│   └── hello-world-8.nf
├── greetings.txt
├── hello-gatk.nf
├── hello-world.nf
└── nextflow.config

Description of contents

The data directory contains the input data we'll use in Part 2: Hello GATK, which uses an example from genomics to demonstrate how to build a simple analysis pipeline. The data is described in detail in that section of the training.

The scripts directory contains the completed workflow scripts that result from each step of the tutorial and are intended to be used as a reference to check your work. The name and number in the filename correspond to the step of the relevant tutorial. For example, the file hello-world-4.nf is the expected result of completing steps 1 through 4 of Part 1: Hello World.

The file greetings.txt is a plain text file used to provide inputs in Part 1: Hello World.

The file hello-gatk.nf is a stub that serves as a starting point to Part 2: Hello GATK. In its initial state, it is NOT a functional workflow script.

The file hello-world.nf is a simple but fully functional workflow script that serves as a starting point to Part 1: Hello World.

The file nextflow.config is a configuration file that sets minimal environment properties.