Orientation

The Gitpod environment contains some test data that will be used in this training course. All software required is already installed and configured in it too.

Note

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

Materials provided

Throughout this training course, we'll be working in the hello-nextflow/ directory.

cd /workspace/gitpod/hello-nextflow

This directory contains all the code files, test data and accessory files you will need. Feel free to explore the contents of this directory; an easy way to see what it contains is the use the tree command (here we generate a table of contents to the second level down).

tree . -L 2

You should see the following output:

Directory contents

/workspace/gitpod/hello-nextflow
├── data
│   ├── bam
│   ├── greetings.csv
│   ├── ref
│   ├── sample_bams.txt
│   └── samplesheet.csv
├── hello-gatk.nf
├── hello-modules.nf
├── hello-nf-test.nf
├── hello-world.nf
├── nextflow.config
└── scripts
    ├── hello-config-1.config
    ├── hello-config-2.config
    ├── hello-config-3.config
    ├── hello-config-4.config
    ├── 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-modules-1.nf
    ├── hello-modules-2.nf
    ├── hello-modules-3.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
    ├── hello-world-9.nf
    ├── modules
    └── nextflow.config

13 directories, 48 files

The data directory contains the input data we'll use in Part 3: Hello Genomics, which uses an example from genomics to demonstrate how to build a simple analysis pipeline. The data are described in detail in that section of the course.

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

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 hello-gatk.nf is a stub that serves as a starting point to Part 3: Hello Genomics. In its initial state, it is NOT a functional workflow script.

The remaining .nf files are functional workflow scripts that serve as starting points for the corresponding parts of the course.

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