nf-configs/README.md

# [![nf-core/configs](docs/images/nfcore-configs_logo.png "nf-core/configs")](https://github.com/nf-core/configs)

[![Lint Status](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)](https://github.com/nf-core/configs/workflows/Configs%20tests/badge.svg)

A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.

## Table of contents

* [Table of contents](#table-of-contents)
* [Using an existing config](#using-an-existing-config)
  * [Configuration and parameters](#configuration-and-parameters)
  * [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config)
* [Checking user hostnames](#checking-user-hostnames)
  * [Testing](#testing)
  * [Documentation](#documentation)
  * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Help](#help)

## Using an existing config

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.

### 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.

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 customize 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/configs`](https://github.com/nf-core/configs/tree/master/conf).

### Offline usage

If you want to use an existing config available in `nf-core/configs`, 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`
or `params.custom_config_base` set to the location of the directory containing the repository files:

```bash
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/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/configs/configs-master/
```

Alternatively, instead of using the configuration profiles from this repository, you can run your
pipeline directly calling the single institutional config file that you need with the `-c` parameter.

```bash
nextflow run /path/to/pipeline/ -c /path/to/my/configs/configs-master/conf/my_config.config
```

> Note that the nf-core/tools helper package has a `download` command to download all required pipeline
> files + singularity containers + institutional configs in one go for you, to make this process easier.

## Adding a new config

If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) 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.

## Checking user hostnames

If your cluster has a set of consistent hostnames, nf-core pipelines can check that users are using your profile.
Add one or more hostname substrings to `params.hostnames` under a key that matches the profile name.
If the user's hostname contains this string at the start of a run or when a run fails and their profile
does not contain the profile name, a warning message will be printed.

### Testing

If you want to add a new custom config file to `nf-core/configs` please test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter.

```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

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.

See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples.

Currently documentation is available for the following systems:

* [AWSBATCH](docs/awsbatch.md)
* [BIGPURPLE](docs/bigpurple.md)
* [BINAC](docs/binac.md)
* [CBE](docs/cbe.md)
* [CCGA](docs/ccga.md)
* [CCGA_DX](/docs/ccga_dx.md)
* [CFC](docs/binac.md)
* [CRICK](docs/crick.md)
* [CZBIOHUB_AWS](docs/czbiohub.md)
* [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md)
* [DENBI_QBIC](docs/denbi_qbic.md)
* [GENOTOUL](docs/genotoul.md)
* [GENOUEST](docs/genouest.md)
* [GIS](docs/gis.md)
* [HEBBE](docs/hebbe.md)
* [KRAKEN](docs/kraken.md)
* [MUNIN](docs/munin.md)
* [PASTEUR](docs/pasteur.md)
* [PHOENIX](docs/phoenix.md)
* [PRINCE](docs/prince.md)
* [SHH](docs/shh.md)
* [UCT_HEX](docs/uct_hex.md)
* [UPPMAX](docs/uppmax.md)
* [UPPMAX_DEVEL](docs/uppmax.md)
* [UZH](docs/uzh.md)

### Uploading to `nf-core/configs`

[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.

Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to the alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions. If you forget to do this, tests will fail and complain about that.

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/configs` 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.

## Help

If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).