diff --git a/README.md b/README.md index d2ae637..934ef12 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![Build Status](https://travis-ci.org/nf-core/configs.svg?branch=master)](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. +A repository for hosting Nextflow configuration files containing custom parameters required to run nf-core pipelines at different Institutions. ## Table of contents @@ -80,7 +80,7 @@ If you want to add a new custom config file to `nf-core/configs` please test tha ```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]' +nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '/path/to/custom.config' ``` ### Documentation @@ -119,7 +119,7 @@ Currently documentation is available for the following systems: ### Uploading to `nf-core/configs` -[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. +[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. @@ -130,7 +130,7 @@ We will be notified automatically when you have created your pull request, and p ## 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. +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. @@ -138,26 +138,24 @@ Instead, we can create a pipeline-specific institutional config file. 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 ``. +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. -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. - -### Pipeline specific documentation +### Pipeline-specific documentation Currently documentation is available for the following pipeline within the specific profile: * sarek * [MUNIN](docs/pipeline/sarek/munin.md) -### Enabling the specific configs within a specific pipeline +### Enabling pipeline-specific configs within a pipeline -:warning: **This has to be done on a fork of the `nf-core/` repository.** +: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: @@ -175,12 +173,16 @@ Commit and push these changes to your local clone on GitHub, and then [create a 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 specific nf-core/configs for the pipeline +### Create the pipeline-specific `nf-core/configs` files -:warning: This has to be done on a fork of the `nf-core/configs` repository. +: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` repository to your own GitHub account. -Within the local clone of your fork, if not already created, create the `pipeline/.config` file, and add your custom profile to the profile scope +[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 { @@ -188,12 +190,24 @@ profiles { } ``` +* `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. +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