# [![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 configuration 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) * [Checking user hostnames](#checking-user-hostnames) * [Testing](#testing) * [Documentation](#documentation) * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) * [Adding a new pipeline-specific config](#adding-a-new-pipeline-specific-config) * [Pipeline-specific documentation](#pipeline-specific-documentation) * [Enabling pipeline-specific configs within a pipeline](#enabling-pipeline-specific-configs-within-a-pipeline) * [Create the pipeline-specific `nf-core/configs` files](#create-the-pipeline-specific-nf-coreconfigs-files) * [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://sylabs.io/singularity/) 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 ` 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_DX](docs/ccga_dx.md) * [CCGA_MED](docs/ccga_med.md) * [CFC](docs/cfc.md) * [CRICK](docs/crick.md) * [CZBIOHUB_AWS](docs/czbiohub.md) * [CZBIOHUB_AWS_HIGHPRIORITY](docs/czbiohub.md) * [DENBI_QBIC](docs/denbi_qbic.md) * [EBC](docs/ebc.md) * [GENOTOUL](docs/genotoul.md) * [GENOUEST](docs/genouest.md) * [GIS](docs/gis.md) * [GOOGLE](docs/google.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) * [UTD_GANYMEDE](docs/utd_ganymede.md) * [UZH](docs/uzh.md) ### Uploading to `nf-core/configs` [Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/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. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error: ```bash Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML. set(['']) ##[error]Process completed with exit code 1. ``` 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. ## Adding a new pipeline-specific config Sometimes it may be desirable to have configuration options for an institute that are specific to a single nf-core pipeline. Such options should not be added to the main institutional config, as this will be applied to all pipelines. Instead, we can create a pipeline-specific institutional config file. :warning: Remember to replace the `` and `` placeholders with the pipeline name and profile name in the following examples Institutional configs work because the pipeline `nextflow.config` file loads the [`nf-core/configs/nfcore_custom.config` config file](https://github.com/nf-core/configs/blob/master/nfcore_custom.config), which in turn loads the institutional configuration file based on the profile `` supplied on the command line. To add in pipeline-specific institutional configs, we add a second `includeConfig` call in the pipeline `nextflow.config` file, which loads the `pipeline/.config` file from the [`nf-core/configs`](https://github.com/nf-core/configs) repo. This file has `` specific institution configuration again with different profiles ``. The pipeline `nextflow.config` file should first load the generic institutional configuration file and then the pipeline-specific institutional configuration file. Each configuration file will add new params and overwrite the params already existing. Note that pipeline-specific configs are not required and should only be added if needed. ### Pipeline-specific documentation Currently documentation is available for the following pipeline within the specific profile: * ampliseq * [BINAC](docs/pipeline/ampliseq/binac.md) * [UPPMAX](docs/pipeline/ampliseq/uppmax.md) * eager * [SHH](docs/pipeline/eager/shh.md) * rnafusion * [MUNIN](docs/pipeline/rnafusion/munin.md) * sarek * [MUNIN](docs/pipeline/sarek/munin.md) * [UPPMAX](docs/pipeline/sarek/uppmax.md) ### Enabling pipeline-specific configs within a pipeline :warning: **This has to be done on a fork of the `nf-core/` repository.** [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/` repository to your own GitHub account. Within the local clone of your fork, if not already present, add the following to `nextflow.config` **after** the code that loads the generic nf-core/configs config file: ```nextflow // Load nf-core/ custom profiles from different Institutions try { includeConfig "${params.custom_config_base}/pipeline/.config" } catch (Exception e) { System.err.println("WARNING: Could not load nf-core/config/ profiles: ${params.custom_config_base}/pipeline/.config") } ``` Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/` GitHub repo with the appropriate information. We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible. ### Create the pipeline-specific `nf-core/configs` files :warning: This has to be done on a fork of the [`nf-core/configs`](https://github.com/nf-core/configs/) repository. [Fork](https://help.github.com/articles/fork-a-repo/) the [`nf-core/configs`](https://github.com/nf-core/configs/) repository to your own GitHub account. And add or edit the following files in the local clone of your fork. * `pipeline/.config` If not already created, create the `pipeline/.config` file, and add your custom profile to the profile scope ```Groovy profiles { { includeConfig "${params.custom_config_base}/conf/pipeline//.config" } } ``` * `conf/pipeline//.config` Add the custom configuration file to the `conf/pipeline//` directory. Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/.config` and set to reasonable values. Users will get information on who wrote the pipeline-specific configuration profile then when executing the nf-core pipeline and can report back if there are things missing for example. * `docs/pipeline//.md` Add the documentation file to the `docs/pipeline//` directory. You will also need to edit and add your custom profile to the [`README.md`](https://github.com/nf-core/configs/blob/master/README.md) file in the top-level directory of the clone. * `README.md` Edit this file, and add the new pipeline-specific institutional profile to the list in the section Pipeline specific documentation 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. In the pull-request description, add a link to the repository specific pull-request(s) that use this new code. Both PRs will need to be merged at the approximately the same time. ## Help If you have any questions or issues please send us a message on [Slack](https://nfcore.slack.com/channels/configs).