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Propose module organization

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See above changes to readme :_)
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README.md
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> DSL2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT OF THIS REPOSITORY MAY CHANGE IN THE NEAR FUTURE! > 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. 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 ## Table of contents
* [Using existing modules](#using-existing-modules) * [Using existing modules](#using-existing-modules)
@ -14,6 +14,21 @@ A repository for hosting nextflow [`DSL2`](https://www.nextflow.io/docs/edge/dsl
* [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules) * [Uploading to `nf-core/modules`](#uploading-to-nf-coremodules)
* [Help](#help) * [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 ## 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. 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.