nextflow-modules

nf-core-compatible Nextflow modules for bioimage analysis tools.

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

The org_path is "bits" which stands for BioImageTools.

Prerequisites

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

Initializing an nf-core pipeline

To install modules from this repository you must have an nf-core-compatible pipeline folder structure. Your pipeline should be called main.nf, and you should have a nextflow.config in the same folder. With the current version (2.10) of nf-core tools, you must also initialize some directory and file structure:

touch .nf-core.yml
mkdir modules

Next, create a modules.json file in that folder like this:

{
    "name": "",
    "homePage": "",
    "repos": {
        "[email protected]:BioImageTools/nextflow-modules.git": {
            "modules": {
            }
        }
    }
}

When you install a module, it may prompt you with some questions the first time through. Just accept the defaults:

Is this repository an nf-core pipeline or a fork of nf-core/modules? pipeline
Would you like me to add this config now? yes

Installing a module

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

nf-core modules -g [email protected]:BioImageTools/nextflow-modules.git install spark/prepare

Installing a subworkflow

nf-core subworkflows -g [email protected]:BioImageTools/nextflow-modules.git install spark_start

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