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# ![nf-core/modules](docs/images/nfcore-modules_logo.png) # ![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! > THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE IN THE NEAR FUTURE!
A repository for hosting Nextflow [`DSL2`](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation. A repository for hosting Nextflow [`DSL2`](https://www.nextflow.io/docs/latest/dsl2.html) module files (see [Terminology](#terminology)) containing tool-specific process definitions and their associated documentation.
## Table of contents ## Table of contents
- [Terminology](#terminology)
- [Using existing modules](#using-existing-modules) - [Using existing modules](#using-existing-modules)
- [Configuration and parameters](#configuration-and-parameters) - [Configuration and parameters](#configuration-and-parameters)
- [Offline usage](#offline-usage) - [Offline usage](#offline-usage)
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- [Testing](#testing) - [Testing](#testing)
- [Documentation](#documentation) - [Documentation](#documentation)
- [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules) - [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
- [Terminology](#terminology)
- [Help](#help) - [Help](#help)
## Terminology
The features offered by Nextflow DSL2 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`. At present, this repository has been created to only host atomic module files that should be added to the `software/` directory along with the required documentation 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 although this may change in the future since well-written sub-workflows will be the most powerful aspect of DSL2.
- *Workflow*: What DSL1 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 DSL1, or by using a combination of DSL2 individual modules and sub-workflows.
## Using existing modules ## Using existing modules
We have written a helper command in the nf-core/tools package that allows you to install any module present in the `software/` directory of this repository. We have written a helper command in the nf-core/tools package that allows you to install any module present in the `software/` directory of this repository.
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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. 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.
## Terminology
The features offered by Nextflow DSL2 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 DSL2 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`. At present, this repository has been created to only host atomic module files that should be added to the `software/` directory along with the required documentation 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 although this may change in the future since well-written sub-workflows will be the most powerful aspect of DSL2.
- *Workflow*: What DSL1 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 DSL1, or by using a combination of DSL2 individual modules and sub-workflows.
## Help ## Help
If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack). If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).