Getting started

Coordinating with others

Let's not duplicate effort:

• Check the module does not exist in nf-core or sanger-tol
• Check there is no pull request or issue open for the module.
• Now you are ready to get started. Let everyone know what you want to work on by creating an issue for a new module

Getting the Git repository

If it's your first module and you don't yet have a checkout of the sanger-tol repository:

git clone [email protected]:sanger-tol/nf-core-modules.git

Otherwise, update it:

cd nf-core-modules
git fetch origin nf-core_master

Then create a new branch for your module, from the freshest master branch:

cd nf-core-modules
# If pushing to sanger-tol/nf-core-modules
git checkout -b <software_tool> origin/main
# If pushing to nf-core/modules
git checkout -b <software_tool> origin/nf-core_master

Writing the module

ℹ️ First of all, you need a Conda environment with Nextflow, nf-core/tools and pytest (Singularity is added to PATH separately). See Shared Conda environments in Tree of Life for instructions on how to use the central one or create yours.

Create a module template with the nf-core tool:

cd nf-core-modules    # if not in there yet
conda activate /software/treeoflife/miniconda3/envs/nf-core_dev
nf-core modules create <software/tool> --dir . --author @github-username --label process_medium --meta

In the command, <software/tool> can be samtools/view or longranger/align. If there is no nesting, then just the <tool> name, like fastqc. If you are not clear, please ask.

If you need help, check our Confluence page with a list of support resources.

Happy Coding 👩‍💻 !