# [nf-core/configs](https://github.com/nf-core/configs) [](https://travis-ci.org/nf-core/configs) A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions. ## 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) * [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 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/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 ` 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 clusters: * [BINAC](docs/binac.md) * [CCGA](docs/ccga.md) * [CFC](docs/binac.md) * [CRICK](docs/crick.md) * [GIS](docs/gis.md) * [HEBBE](docs/hebbe.md) * [MENDEL](docs/mendel.md) * [MUNIN](docs/munin.md) * [PHOENIX](docs/phoenix.md) * [SHH](docs/shh.md) * [UCT_HEX](docs/uct_hex.md) * [UPPMAX-DEVEL](docs/uppmax-devel.md) * [UPPMAX](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. 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-core-invite.herokuapp.com/).