How to guide
Set up
Requirements:
- A GitHub account
- Installed on your chosen development environment:
Clone the template
- Open the DSL2 template repository on GitHub
- Select the Use this template box and create a new repository
- Name your repository, ending in
-nf(this is required by cookiecutter gh action) - Select the Create repository from template box
Once you create a new repository using this template, a GitHub Action workflow will automatically be deployed. This workflow will populate your new repository with the skeleton template directory.
We recommend working in a development environment like VS Code to work with this template. If you’re working with VS Code, use the nf-core-extensionpack for some nice features like syntax highlighting. You can clone your copy of the template to your environment using git.
For example:
git clone https://github.com/georgiesamaha/myWorkflow-nf.gitDownload Nextflow
Depending on the system you’re working on there are a few options for installing and running Nextflow including reproducible options like bioconda and Singularity. See here for installation instructions.
Once you have installed Nextflow, you can configure it to run on your system. See here for some set up tips.
Use the template
This template currently contains 3 processes as as part of the demo workflow. To use this workflow yourself, you will need to delete any processes associated with the demo. Each line of code inside the nextflow.config and main.nf associated with the demo workflow is prefixed by a comment line // DEMO CODE: DELETE FOR YOUR OWN WORKFLOWS.
Delete the 3 demo process files (modules/check_input.nf, modules/group_samples.nf, modules/generate_report.nf) and use the template_process.nf to structure your own processes.
See the template_components sections in this user guide for what how to use all directories and files provided in this template.