# [![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) - [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 institutional documentation](#pipeline-specific-institutional-documentation) - [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 To use nf-core pipelines offline, we recommend using the `nf-core download` helper tool. This will download both the pipeline files and also the config profiles from `nf-core/configs`. The pipeline files are then edited to load the configs from their relative file path correctly. ```bash # Download the workflow + transfer to offline cluster nf-core download rnaseq scp nf-core-rnaseq-3.0.tar.gz me@myserver.com:/path/to/workflows # or however you prefer to transfer files to your offline cluster # Connect to offline cluster ssh me@myserver.com # Extract workflow files cd /path/to/workflows tar -xzf nf-core-rnaseq-3.0.tar.gz # Run workflow cd /path/to/data nextflow run /path/to/workflows/nf-core-rnaseq-3.0/workflow -profile mycluster ``` If required, you can instead download the nf-core/configs files yourself and customise the `--custom_config_base` / `params.custom_config_base` parameter in each pipeline to to set to the location of the configs directory. ## 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. Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](Using an existing config)), and then continuing with the next steps. N.B. In your config file, 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. N.B. If you try to specify a shell environment variable within your profile, in some cases you may get an error during testing of something like `Unknown config attribute env.USER_SCRATCH -- check config file: /home/runner/work/configs/configs/nextflow.config` (where the bash environment variable is `$USER_SCRATCH`). This is because the github runner will not have your institutional environment variables set. To fix this you can define this as an internal variable, and set a fallback value for that variable. A good example is in the [VSC_UGENT profile](`https://github.com/nf-core/configs/blob/69468e7ca769643b151a6cfd1ab24185fc341c06/conf/vsc_ugent.config#L2`). ### 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: - [ABIMS](docs/abims.md) - [ADCRA](docs/adcra.md) - [ALICE](docs/alice.md) - [AWSBATCH](docs/awsbatch.md) - [AWS_TOWER](docs/aws_tower.md) - [AZUREBATCH](docs/azurebatch.md) - [BIGPURPLE](docs/bigpurple.md) - [BI](docs/bi.md) - [BINAC](docs/binac.md) - [BIOHPC_GEN](docs/biohpc_gen.md) - [CAMBRIDGE](docs/cambridge.md) - [CBE](docs/cbe.md) - [CCGA_DX](docs/ccga_dx.md) - [CCGA_MED](docs/ccga_med.md) - [Cedars-Sinai](docs/cedars.md) - [CFC](docs/cfc.md) - [CHEAHA](docs/cheaha.md) - [Computerome](docs/computerome.md) - [CRICK](docs/crick.md) - [Cancer Research UK Manchester Institute](docs/crukmi.md) - [CZBIOHUB_AWS](docs/czbiohub.md) - [DENBI_QBIC](docs/denbi_qbic.md) - [EBC](docs/ebc.md) - [EVA](docs/eva.md) - [FGCZ](docs/fgcz.md) - [GENOTOUL](docs/genotoul.md) - [GENOUEST](docs/genouest.md) - [GIS](docs/gis.md) - [GOOGLE](docs/google.md) - [HASTA](docs/hasta.md) - [HEBBE](docs/hebbe.md) - [HKI](docs/hki.md) - [ICR_DAVROS](docs/icr_davros.md) - [IMPERIAL](docs/imperial.md) - [JAX](docs/jax.md) - [KU SUND DANGPU](docs/ku_sund_dangpu.md) - [LUGH](docs/lugh.md) - [MAESTRO](docs/maestro.md) - [Mana](docs/mana.md) - [MARVIN](docs/marvin.md) - [MEDAIR](docs/medair.md) - [MJOLNIR_GLOBE](docs/mjolnir_globe.md) - [MPCDF](docs/mpcdf.md) - [MUNIN](docs/munin.md) - [NU_GENOMICS](docs/nu_genomics.md) - [NIHBIOWULF](docs/nihbiowulf.md) - [OIST](docs/oist.md) - [PASTEUR](docs/pasteur.md) - [PHOENIX](docs/phoenix.md) - [PRINCE](docs/prince.md) - [ROSALIND](docs/rosalind.md) - [SAGE BIONETWORKS](docs/sage.md) - [SANGER](docs/sanger.md) - [SBC_SHARC](docs/sbc_sharc.md) - [SEG_GLOBE](docs/seg_globe.md) - [TIGEM](docs/tigem.md) - [UCT_HPC](docs/uct_hpc.md) - [UNIBE_IBU](docs/unibe_ibu.md) - [UPPMAX](docs/uppmax.md) - [UTD_GANYMEDE](docs/utd_ganymede.md) - [UTD_SYSBIO](docs/utd_sysbio.md) - [UZH](docs/uzh.md) - [VAI](docs/vai.md) - [VSC_UGENT](docs/vsc_ugent.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 - **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory - **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 - **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 (under strategy matrix) 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. > The following steps are similar to the instructions for standard institutional config, however using `pipeline` variants of folders e.g., `conf/pipeline/` or under `pipeline/` :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 institutional documentation Currently documentation is available for the following pipelines within specific profiles: - ampliseq - [BINAC](docs/pipeline/ampliseq/binac.md) - [UPPMAX](docs/pipeline/ampliseq/uppmax.md) - atacseq - [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md) - chipseq - [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md) - demultiplex - [AWS_TOWER](docs/pipeline/demultiplex/aws_tower.md) - eager - [EVA](docs/pipeline/eager/eva.md) - mag - [EVA](docs/pipeline/mag/eva.md) - rnafusion - [HASTA](docs/pipeline/rnafusion/hasta.md) - [MUNIN](docs/pipeline/rnafusion/munin.md) - rnaseq - [SBC_SHARC](docs/pipeline/rnaseq/sbc_sharc.md) - rnavar - [MUNIN](docs/pipeline/rnavar/munin.md) - sarek - [Cancer Research UK Manchester Institute](docs/pipeline/sarek/crukmi.md) - [MUNIN](docs/pipeline/sarek/munin.md) - [SBC_SHARC](docs/pipeline/sarek/sbc_sharc.md) - [UPPMAX](docs/pipeline/sarek/uppmax.md) - taxprofiler - [EVA](docs/pipeline/taxprofiler/eva.md) - [hasta](docs/pipeline/taxprofiler/hasta.md) ### Pipeline-specific documentation Currently documentation is available for the following pipeline: - viralrecon - [genomes](docs/pipeline/viralrecon/genomes.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).