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Add docs as to what exactly you have to do when adding new config

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James A. Fellows Yates 2021-04-07 20:24:55 +02:00 committed by GitHub
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README.md
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@ -67,7 +67,15 @@ If you decide to upload your custom config file to `nf-core/configs` then this w
You will simply have to specify `-profile <config_name>` in the command used to run the pipeline. You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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. When adding a new config you will need to either add and/or update the following files:
* **Add** your institutional config itself under the `conf/` directory accordingly
* **Add** documentation for your institutional config under the `docs/` directory
* **Update** the file `nfcore_custom.config` to include your config in list of nf-core institutional configs
* **Update** the file `README.md` to include your config documentation within the list of configs docs
* **Update** the `.github/workflows/main/yml` to include your config in the profile strategy matrix for the GitHub actions CI tests
N.B. In your config file under `confg/`, 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. 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.
### Checking user hostnames ### Checking user hostnames
@ -156,6 +164,8 @@ Sometimes it may be desirable to have configuration options for an institute tha
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.
> The following steps are similar to the instructions for standard institutional profilers, however using `pipeline` variants of folders e.g., `conf/pipeline/` or under `pipeline/`
:warning: Remember to replace the `<PIPELINE>` and `<PROFILE>` placeholders with the pipeline name and profile name in the following examples :warning: Remember to replace the `<PIPELINE>` and `<PROFILE>` 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 `<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.