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MaxUlysse 2019-11-20 14:34:06 +01:00
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@ -115,6 +115,50 @@ 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.
## Adding a new pipeline specific config
Follow the previous guidelines to create a nf-core/configs, update the pipeline specific documentation, and create the necessary files.
Replace `<PIPELINE>` with the pipeline name for all the instructions in this guidelines.
In a similar manner, replace `<PROFILE>` by the name of the profile.
### Pipeline specific documentation
Currently documentation is available for the following pipelines within the specific profile:
* sarek
* [MUNIN](docs/pipeline/sarek/munin.md)
### Enabling the specific configs within a specific PIPELINE
> This has to be done on a fork of the `nf-core/<PIPELINE>` repository.
If not already present, add to `nextflow.config`
```Groovy
// Load nf-core/<PIPELINE> custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/pipeline/<PIPELINE>.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/<PIPELINE> profiles: ${params.custom_config_base}/pipeline/<PIPELINE>.config")
}
```
### Create the specific nf-core/configs for the pipeline
> This has to be done on a fork of the `nf-core/configs` repository.
If not already created, add the `pipeline/<PIPELINE>.config` file, and add the profile <PROFILE> to the profile scope
```Groovy
profiles {
<PROFILE> { includeConfig "${params.custom_config_base}/conf/pipeline/<PIPELINE>/<PROFILE>.config" }
}
```
Add the `conf/pipeline/<PIPELINE>/<PROFILE>.config` file with all pipeline specific params, `withLabel` or any other configuration profile.
Add the `docs/pipeline/<PIPELINE>/<PROFILE>.md` file with documentation on what are the specificity of this configs.
## Help
If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack).