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 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 features offered by Nextflow DSL 2 can be used in various ways depending on the granularity with which you would like to write pipelines. Please see the listing below for the hierarchy and associated terminology we have decided to use when referring to DSL 2 components:

- *Module*: A `process`that can be used within different pipelines and is as atomic as possible i.e. cannot be split into another module. An example of this would be a module file containing the process definition for a single tool such as `FastQC`. This repository has been created to only host atomic module files that should be added to the `tools` sub-directory along with the required documentation, software and tests.
- *Sub-workflow*: A chain of multiple modules that offer a higher-level of functionality within the context of a pipeline. For example, a sub-workflow to run multiple QC tools with FastQ files as input. Sub-workflows should be shipped with the pipeline implementation and if required they should be shared amongst different pipelines directly from there. As it stands, this repository will not host sub-workflows.
- *Workflow*: What DSL 1 users would consider an end-to-end pipeline. For example, from one or more inputs to a series of outputs. This can either be implemented using a large monolithic script as with DSL 1, or by using a combination of DSL 2 individual modules and sub-workflows.

## 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/chipseq`](https://github.com/nf-core/chipseq/tree/dev) (work in progress)

### 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/software`](https://github.com/nf-core/modules/tree/master/software)
for examples.

**The definition and standards for module files are still under discussion
amongst the community. Currently the following points have been agreed on:**

The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in [RFC 2119](https://tools.ietf.org/html/rfc2119).

### Defining inputs, outputs and parameters
- A module file SHOULD only define inputs and outputs as parameters. Additionally,
    - it MUST define threads or resources where required for a particular process using `task.cpus`
    - ~~it MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_args` parameter.~~
    - it MUST be possible to pass additional parameters as a [nextflow Map](https://www.nextflow.io/docs/latest/script.html#maps) through an additional input channel `val(options)` [Details require discussion].
    - All NGS modules MUST accept a triplet [name, single_end, reads] as input. The single-end boolean values MUST be specified through the input channel and not inferred from the data e.g. [here](https://github.com/nf-core/tools/blob/028a9b3f9d1ad044e879a1de13d3c3a25a06b9a7/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/modules/nf-core/fastqc.nf#L13).
- Process names MUST be all uppercase.
- Each process MUST emit a file `<TOOL>.version.txt` containing a single line with the software's version in the format `v<VERSION_NUMBER>`.
- All outputs MUST be named using `emit`.
- A Process MUST NOT contain a `when` statement.
- Optional inputs need development on the nextflow side. In the meanwhile, "fake files" MAY be used to work around this issue.

### Atomicity
- Software that can be piped together SHOULD be added to separate module files unless there is an run-time, storage advantage in implementing in this way e.g. `bwa mem | samtools view -C -T ref.fasta` to output CRAM instead of SAM.

### Resource requirements
- Each module MUST define a label `process_low`, `process_medium` or `process_high` to declare resource requirements. (*These flags will be ignored outside of nf-core and the pipeline developer is free to define adequate resource requirements*)

### Publishing results
- The module MUST accept the parameters `params.out_dir` and `params.publish_dir` and MUST publish results into `${params.out_dir}/${params.publish_dir}`.
- The `publishDirMode` MUST be configurable via `params.publish_dir_mode`
- The module MUST accept a parameter `params.publish_results` accepting at least
    - `"none"`, to publish no files at all,
    - a glob pattern which is initalized to a sensible default value.

    It MAY accept `"logs"` to publish relevant log files, or other flags, if applicable.

- To ensure consistent naming, files SHOULD be renamed according to the `$name` variable before returning them.

### Testing
- Every module MUST be tested by adding a test workflow with a toy dataset.
- Test data MUST be stored within this repo. It is RECOMMENDED to re-use generic files from `tests/data` by symlinking them into the test directory of the module. Specific files MUST be added to the test-directory directly. Test files MUST be kept as tiny as possible.

### Software requirements
- Software requirements SHOULD be declared in a conda `environment.yml` file, including exact version numbers. Additionally, there MUST be a `Dockerfile` that containerizes the environment, or packages the software if conda is not available.
- Docker containers MUST BE identified by their `sha256(Dockerfile + environment.yml)`.
- Each module must have it's own `Dockerfile` and `environment.yml` file
    - Care should be taken to maintain identical files for subcommands that use the same software. Then the hash tag will be the same and they will be implicitly re-used across subcommands.

### File formats
- Wherever possible, [CRAM](https://en.wikipedia.org/wiki/CRAM_(file_format)) files SHOULD be used over BAM files.
- Wherever possible, FASTQ files SHOULD be compressed using gzip.

### Documentation
- A module MUST be documented in the `meta.yml` file. It MUST document `params`, `input` and `output`. `input` and `output` MUST be a nested list. [Exact detail need to be elaborated. ]

### 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/software`](https://github.com/nf-core/modules/tree/master/software) 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).