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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)
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.
@ -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.
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.
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/<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/<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.
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/<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/<PIPELINE>.config`
If not already created, create the `pipeline/<PIPELINE>.config` file, and add your custom profile to the profile scope
```Groovy
profiles {
@ -188,12 +190,24 @@ profiles {
}
```
* `conf/pipeline/<PIPELINE>/<PROFILE>.config`
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.
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