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Add example tools

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@ -5,13 +5,11 @@
> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
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 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)
@ -22,6 +20,8 @@ A repository for hosting Nextflow [`DSL2`](https://www.nextflow.io/docs/latest/d
## Using existing modules
The module files hosted in this repository define a set of processes for software tools such as `fastqc`, `bwa`, `samtools` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
We have written a helper command in the `nf-core/tools` package that uses the GitHub API to obtain the relevant information for the module files present in the `software/` directory of this repository. This includes using `git` commit hashes to track changes for reproducibility purposes, and to download and install all of the relevant module files.
1. [Install](https://github.com/nf-core/tools#installation) the latest version of `nf-core/tools` (`>=1.10.2`)
@ -96,40 +96,16 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
check Check that imported module code has not been modified. (NOT YET IMPLEMENTED)
```
### 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
> The definition and standards for module files are still under discussion amongst the nf-core community**
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
@ -208,3 +184,31 @@ If you use the module files in this repository for your analysis please you can
>
> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
<!---
### 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.
-->