Getting Started

Let the user know how to get started with the workflow. This should mirror the section in your README, or the README should point them here.

Prerequisites

Define the software and hardware requirements needed to run the workflow.

The workflow requires the following software:

  • Pixi: Creates the environment for running the workflow.
  • Git: Version control
  • A container runtime: Docker (for local testing) or Singularity/Apptainer (recommended for HPC).

Include expected resource usage on a typical dataset if possible, such as memory, CPU, runtime, and disk usage.

This workflow can run on standard HPC nodes with at least 16 GB of RAM and 4 CPU cores. Typical runtime for a whole-exome sequencing sample pair is approximately 6-8 hours, depending on the dataset size and computational resources allocated.

How to run/install

Supply a tiny dataset for testing purposes, along with example commands to run the workflow.

Nextflow Example:

# Open a Pixi shell to create an environment for running the workflow.
pixi shell
# Runs a small, defined test case using pre-configured containers.
nextflow run main.nf -profile test,docker

Snakemake Example:

# Runs with a minimal config file, leveraging Conda environments.
snakemake --use-conda -j 4 --configfile config/test_config.yaml