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## Using an existing module ## Using an existing module
The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation. 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/rnaseq`](https://github.com/nf-core/rnaseq/pull/162)
### Configuration and parameters ### Configuration and parameters
The config files hosted in this repository define a set of parameters which are specific to compute environments at different Institutions but generic enough to be used with all nf-core pipelines. The module files hosted in this repository define a set of processes for software tools such as `fastc`, `trimgalore`, `bwa` etc. This allows you to share and add common functionality across multiple pipelines in a modular fashion.
All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customise the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines.
You should be able to get a good idea as to how other people are customising the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/modules`](https://github.com/nf-core/modules/tree/master/conf).
### Offline usage ### Offline usage
If you want to use an existing config available in `nf-core/modules`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. Then run the pipeline with `--custom_config_base` 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:
or `params.custom_config_base` set to the location of the directory containing the repository files:
```bash ```bash
## Download and unzip the config files include /path/to/downloaded/modules/directory/
cd /path/to/my/modules
wget https://github.com/nf-core/modules/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/modules/modules-master/
``` ```
Alternatively, instead of using the configuration profiles from this repository, you can run your Then you can run the pipeline by directly passing the additional config file with the `-c` parameter:
pipeline directly calling the single institutional config file that you need with the `-c` parameter.
```bash ```bash
nextflow run /path/to/pipeline/ -c /path/to/my/modules/modules-master/conf/my_config.config 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 > Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional modules in one go for you, to make this process easier. > files + singularity containers + institutional configs + modules in one go for you, to make this process easier.
## Adding a new config ## Adding a new module file
If you decide to upload your module file to `nf-core/module` 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 community. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. See [`nf-core/modules`](https://github.com/nf-core/modules/tree/master/conf) for examples. 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`](https://github.com/nf-core/modules/tree/master/nf) for examples.
Please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values. Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example. The definition and standards for module files is still under discussion amongst the community but hopefully, a description should be added here soon!
### Testing ### Testing
If you want to add a new custom config file to `nf-core/modules` please test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter. If you want to add a new module config file to `nf-core/modules` please test that your pipeline of choice runs as expected by using the [`-include`](https://www.nextflow.io/docs/edge/dsl2.html#modules-include) statement with a local version of the module file.
```bash
## Example command for nf-core/rnaseq
nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]'
```
### Documentation ### Documentation
You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation. You might orientate yourself using the [Template](docs/template.md) that we provide and filling out the information for your cluster there. You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the module file and extensive links to documentation for the tool(s) used in the module file. You can use the provided [`template.md`](docs/template.md) to guide you as to how to do this appropriately.
See [`nf-core/modules/docs`](https://github.com/nf-core/modules/tree/master/docs) for examples. See [`nf-core/modules/docs`](https://github.com/nf-core/modules/tree/master/docs) for examples.
### Uploading to `nf-core/modules` ### 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 custom config file to the [`modules/`](https://github.com/nf-core/modules/tree/master/modules) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/modules/tree/master/docs) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively. [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/`](https://github.com/nf-core/modules/tree/master/nf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/modules/tree/master/docs) 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 the `nf-core/modules` GitHub repo with the appropriate information. 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. 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.

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# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON!

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# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON!

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# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON!