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@ -2,7 +2,7 @@
[![Build Status](https://travis-ci.org/nf-core/configs.svg?branch=master)](https://travis-ci.org/nf-core/configs) [![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 ## 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 ```bash
## Example command for nf-core/rnaseq ## 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 ### Documentation
@ -119,7 +119,7 @@ Currently documentation is available for the following systems:
### Uploading to `nf-core/configs` ### 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. 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 [`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. 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 ## 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. 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. 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 `<PROFILE>` supplied on the command line. 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 `<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/<PIPELINE>.config` file from the [`nf-core/configs`](https://github.com/nf-core/configs) repo. This file has `<PIPELINE>` specific institution configuration again with different profiles `<PROFILE>`. To add in pipeline-specific institutional configs, we add a second `includeConfig` call in the pipeline `nextflow.config` file, which loads the `pipeline/<PIPELINE>.config` file from the [`nf-core/configs`](https://github.com/nf-core/configs) repo.
This file has `<PIPELINE>` specific institution configuration again with different profiles `<PROFILE>`.
The pipeline `nextflow.config` file should first load the generic institutional configuration file and then the pipeline-specific institutional configuration file. 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. 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. 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/<PIPELINE>.config` and set to reasonable values. ### Pipeline-specific documentation
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
Currently documentation is available for the following pipeline within the specific profile: Currently documentation is available for the following pipeline within the specific profile:
* sarek * sarek
* [MUNIN](docs/pipeline/sarek/munin.md) * [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/<PIPELINE>` repository.** :warning: **This has to be done on a fork of the `nf-core/<PIPELINE>` repository.**
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/<PIPELINE>` repository to your own GitHub account. [Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/<PIPELINE>` 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: 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. 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. [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, if not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope And add or edit the following files in the local clone of your fork.
* `pipeline/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
```Groovy ```Groovy
profiles { profiles {
@ -188,12 +190,24 @@ profiles {
} }
``` ```
* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory. Add the custom configuration file to the `conf/pipeline/<PIPELINE>/` directory.
Make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` to the top of `pipeline/<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/<PIPELINE>/<PROFILE>.md`
Add the documentation file to the `docs/pipeline/<PIPELINE>/` directory. Add the documentation file to the `docs/pipeline/<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. 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. 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 ## Help