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# ![nf-core/modules](docs/images/nfcore-modules_logo.png) # ![nf-core/modules](docs/images/nfcore-modules_logo.png)
> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE IN THE NEAR FUTURE! > THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE!
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. 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.
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## 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:
1. [Install](https://github.com/nf-core/tools#installation) the latest version of nf-core/tools (`>=1.10.2`) 1. [Install](https://github.com/nf-core/tools#installation) the latest version of `nf-core/tools` (`>=1.10.2`)
2. List the available modules 2. List the available modules:
```console ```console
$ nf-core modules list $ nf-core modules list
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..truncated.. ..truncated..
``` ```
3. Install the module in the pipeline directory:
```console
$ nf-core modules install . fastqc
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`._,._,'
nf-core/tools version 1.10.2
INFO Installing fastqc modules.py:62
INFO Downloaded 3 files to ./modules/nf-core/software/fastqc modules.py:97
```
We have plans to add other utility commands to help developers install and maintain modules downloaded from this repository.
```console
$ nf-core modules --help
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`._,._,'
nf-core/tools version 1.10.2
Usage: nf-core modules [OPTIONS] COMMAND [ARGS]...
Work with the nf-core/modules software wrappers.
Tools to manage DSL 2 nf-core/modules software wrapper imports.
Options:
-r, --repository TEXT GitHub repository hosting software wrapper modules.
-b, --branch TEXT Modules GitHub repo git branch to use.
--help Show this message and exit.
Commands:
list List available software modules.
install Add a DSL2 software wrapper module to a pipeline.
update Update one or all software wrapper modules. (NOT YET IMPLEMENTED)
remove Remove a software wrapper from a pipeline. (NOT YET IMPLEMENTED)
check Check that imported module code has not been modified. (NOT YET IMPLEMENTED)
```
### Configuration and parameters ### 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 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.