Nextflow modules

This repository holds reusable modules, subworkflows that are used in Janelia Nextflow pipelines.

The repository is formatted to be compatible with nf-core tooling, in particular the module system.

Prerequisites

You must install nf-core tools in your environment before you can install modules from this repository.

List modules

nf-core modules -g JaneliaSciComp/nextflow-modules list remote

Installing a module

To install a module into a pipeline, use the modules install command, e.g.:

nf-core modules -g JaneliaSciComp/nextflow-modules install spark/prepare

Installing a subworkflow

nf-core subworkflows -g JaneliaSciComp/nextflow-modules install spark_start

This will install the subworkflow and all of its dependencies including the spark_cluster subworkflow and all necessary modules.