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Ensembl Nextflow modules

nextflow_modules is a centralized repository for reusable Nextflow modules, designed to be shared across multiple pipelines. This approach simplifies maintenance and updates by consolidating modules in one location. The repository adheres to the nf-core structure and follows Nextflow's coding conventions, ensuring consistency and compatibility with established standards.

Purpose

A collection of shared Nextflow modules for Ensembl teams:

  • Facilitates collaboration by providing reusable components across teams.
  • Simplifies module usage with tools like nf-core modules and nf-core subworkflows.
  • Avoid Duplication of effort by sharing modules.

Example Usage

nf-core modules --git-remote [email protected]:Ensembl/nextflow_modules.git install tool/subtool
nf-core subworkflows --git-remote [email protected]:Ensembl/nextflow_modules.git install tool/subtool

Initial Setup

The repository contains a pre-defined structure (see above) with some example modules to serve as templates.

Steps for Adding New Modules

  1. Check Existing Modules

    Verify if the required module is already available in nf-core modules and can be directly used.

  2. Create a New Module

    Use nf-core modules create to generate a module template.

    nf-core modules create tool/subtool --author '@ensembl-dev' --label process_low --meta

    Note: Module names must only contain lowercase letters and we must not use the same name for another module. Names with non-lowercase letters (e.g., database/db-factory) will automatically be converted (e.g., database/dbfactory).

  3. Add Module Testing

    Install nf-test and create nf-test for testing using stub data. If required utilize data from test-datasets and update the path in the test_config.

    Note: We have only added minimum tests. You should add more tests as per your module's functionality.

  4. Update Metadata

    Add relevant information in the meta.yml file.

Module Guidelines

Modules in the repository should:

  • Be sensible and scoped to a specific purpose.

  • Be scoped to run only a single tool or functionality.

  • Avoid sharing private information.

  • Be self-contained, with distinct input and output.

  • Have clear and descriptive names that reflect their functionality.

  • Include tags linked to unique IDs and ideally have the first input as a tuple.

     process SOME_MODULE {
 	    tag "$meta.id"
    ...
 }

    Refer to the Meta Map Documentation for additional details.