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Nextflow - from zero2hero practicals

Welcome to the practical exercises for the Nextflow - from zero2hero course!

This folder contains all the code examples used during training. The practicals are organized by day and then in sections for each day, following the course schedule. Each section folder will contain a README.md file with detailed instructions for the practical exercises and eventually additional reference material.

Before you begin

Before you start the practicals, please connect to the HT HPC system and make sure you have the following prerequisites in place:

  1. You can read from the course training folder: /project/nextflow_zero2hero/. Please try ls /project/nextflow_zero2hero/ to verify you have access.
  2. You can load the Nextflow module by running: module load nextflow/25.04.3.
  3. You can load the Singularity module by running: module load singularity.

Setup your working space

It's recommended to create your own working directory to store your practical exercises.

For example, you can create a directory in your home folder or in your group folder. For example:

# Create a directory in your home folder
mkdir -p ~/nextflow_zero2hero_practicals
cd ~/nextflow_zero2hero_practicals

# Or create a directory in your group folder
mkdir -p /group/your_group/your_username/nextflow_zero2hero_practicals
cd /group/your_group/your_username/nextflow_zero2hero_practicals

Now please move into your working directory and clone the course repository there:

git clone https://github.com/HTGenomeAnalysisUnit/nextflow-zero2hero.git

You should see a new folder named nextflow-zero2hero created in your working directory containing all the course materials.

Also create a a dedicated practicals_outputs folder in there where you will actually run the practical exercises, store your exercise files and outputs.

You are now ready to start the practical exercises!

Navigate to the appropriate day and section folder in the practicals folder to begin.

You are free to modify files in your local copy of the repository as needed for the practicals.

Run the exercises

It's generally good practice to create a dedicated working directory for each pipeline you execute, so that the parameters, logs, and outputs are organized and do not interfere with each other.

We suggest creating a dedicated folder for each practical exercise.

For example, assuming you configured a working folder for this course in /group/mygroup/myuser/nextflow_training/, and you create a dedicated practicals_outputs folder in there, navigate to /group/mygroup/myuser/nextflow_training/practicals_outputs and inside create a folder for each specific practical exercise as we progress.

How to run the practicals on HT HPC

  1. Before starting tests and runs, get an interactive session on a compute node with sufficient resources. An example command is below, you can adjust the parameters as needed (-c for number of CPU cores, --mem for memory, -J for job name) and suggestion will be given during the practicals:
srun --wait=0 --pty -p cpu-interactive -c 1 --mem 4G -J nxf_training /bin/bash
  1. Load the Nextflow module and the Singularity module in your interactive session:
module load singularity
module load nextflow/25.04.3