nf-core_modules/README.md

# ![nf-core/modules](docs/images/nfcore-modules_logo.png)

> DSL2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT OF THIS REPOSITORY MAY CHANGE IN THE NEAR FUTURE!

A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl2.htmlhttps://www.nextflow.io/docs/edge/dsl2.html) module files and subworkflows containing tool-specific process definitions and their associated documentation.

## Table of contents
* [Using existing modules](#using-existing-modules)
    * [Configuration and parameters](#configuration-and-parameters)
    * [Offline usage](#offline-usage)
* [Adding a new module file](#adding-a-new-module-file)
    * [Testing](#testing)
    * [Documentation](#documentation)
    * [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
* [Help](#help)

## Terminology

The DSLv2 features for Nextflow are new for everyone and not just beginners. We discussed some terminology terms to discuss things related to modules & subworkflows more appropriately:

* *Module*: An "atomic" module (one thing), e.g. a reusable process from an old pipeline that can be used between different pipelines
* *Subworkflow*: A combined set of modules, that do e.g. preprocessing for a much bigger pipeline. A good example could be a QC subworkflow for FastQ input, that could be (re-) used across multiple pipelines
* *Workflow*: What DSLv1 users would consider a pipeline, e.g. from input to potentially complex output. Can either consist of individual modules, a large monolithic script as in DSLv1 or a combination of subworkflows (or any combination of these three). 

## Organization of repository

* Modules should end up in the subdirectory `modules`
* Subworkflows that are of general interest should end up in `subworkflows` IF they are useful for multiple pipelines (which will be clarified via Review)

Individual pipelines that want to utilize subworkflows to keep their code base cleaner, should probably start implementing subworkflows and then decide / find out which parts can be made accessible to a broader audience here.

## Using existing modules

The Nextflow [`include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement can be used within your pipelines in order to load module files that you have available locally.

You should be able to get a good idea as to how other people are using module files by looking at pipelines available in nf-core e.g. [`nf-core/rnaseq`](https://github.com/nf-core/rnaseq/pull/162)

### Configuration and parameters

The module files hosted in this repository define a set of processes for software tools such as `fastqc`, `trimgalore`, `bwa` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.

> The definition and standards for module files are still under discussion amongst the community but hopefully, a description should be added here soon!

### Offline usage

If you want to use an existing module file available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the repository (e.g. `git clone https://github.com/nf-core/modules.git`) and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline by creating a custom config file called e.g. `custom_module.conf` containing the following information:

```bash
include /path/to/downloaded/modules/directory/
```

Then you can run the pipeline by directly passing the additional config file with the `-c` parameter:

```bash
nextflow run /path/to/pipeline/ -c /path/to/custom_module.conf
```

> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional configs + modules in one go for you, to make this process easier.

## Adding a new module file

If you decide to upload your module file to `nf-core/modules` then this will ensure that it will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within the Nextflow community! See [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) for examples.

> The definition and standards for module files are still under discussion amongst the community but hopefully, a description should be added here soon!

### Testing

If you want to add a new module config file to `nf-core/modules` please test that your pipeline of choice runs as expected by using the [`-include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement with a local version of the module file.

### Documentation

Please add some documentation to the top of the module file in the form of native Nextflow comments. This has to be specified in a particular format as you will be able to see from other examples in the [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) directory.

### Uploading to `nf-core/modules`

[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively.

Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on `nf-core/modules` GitHub repo with the appropriate information.

We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.

## Help

If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).