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Orientation

See the whole playlist on the Nextflow YouTube channel.

GitHub Codespaces

The GitHub Codespaces environment contains all the software, code and data necessary to work through this training course, so you don't need to install anything yourself. However, you do need a (free) GitHub account to log in, and you should take a few minutes to familiarize yourself with the interface.

If you have not yet done so, please go through the Environment Setup mini-course before going any further.

Working directory

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

Change directory now by running this command in the terminal:

cd hello-nextflow/

Tip

If for whatever reason you move out of this directory, you can always use the full path to return to it, assuming you're running this within the Github Codespaces training environment:

cd /workspaces/training/hello-nextflow

Now let's have a look at the contents of this directory.

Materials provided

You can explore the contents of this directory by using the file explorer on the left-hand side of the training workspace. Alternatively, you can use the tree command.

Throughout the course, we use the output of tree to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity.

Here we generate a table of contents to the second level down:

tree . -L 2

If you run this inside hello-nextflow, you should see the following output:

Directory contents
.
├── greetings.csv
├── hello-channels.nf
├── hello-config.nf
├── hello-containers.nf
├── hello-modules.nf
├── hello-workflow.nf
├── hello-world.nf
├── nextflow.config
├── solutions
│   ├── 1-hello-world
│   ├── 2-hello-channels
│   ├── 3-hello-workflow
│   ├── 4-hello-modules
│   ├── 5-hello-containers
│   └── 6-hello-config
└── test-params.json

7 directories, 9 files

Here's a summary of what you should know to get started:

  • The .nf files are workflow scripts that are named based on what part of the course they're used in.

  • The file nextflow.config is a configuration file that sets minimal environment properties. You can ignore it for now.

  • The file greetings.csv contains input data we'll use in most of the course. It is described in Part 1, when we introduce it for the first time.

  • The file test-params.json is a file we'll use in Part 6. You can ignore it for now.

  • The solutions 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.

Now, to begin the course, click on the arrow in the bottom right corner of this page.