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Add docs as to what exactly you have to do when adding new config
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README.md
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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
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You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
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You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
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See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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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.
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When adding a new config you will need to either add and/or update the following files:
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* **Add** your institutional config itself under the `conf/` directory accordingly
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* **Add** documentation for your institutional config under the `docs/` directory
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* **Update** the file `nfcore_custom.config` to include your config in list of nf-core institutional configs
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* **Update** the file `README.md` to include your config documentation within the list of configs docs
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* **Update** the `.github/workflows/main/yml` to include your config in the profile strategy matrix for the GitHub actions CI tests
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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.
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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.
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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.
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### Checking user hostnames
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### Checking user hostnames
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@ -156,6 +164,8 @@ Sometimes it may be desirable to have configuration options for an institute tha
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Such options should not be added to the main institutional config, as this will be applied to all pipelines.
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Such options should not be added to the main institutional config, as this will be applied to all pipelines.
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Instead, we can create a pipeline-specific institutional config file.
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Instead, we can create a pipeline-specific institutional config file.
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> 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/`
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:warning: Remember to replace the `<PIPELINE>` and `<PROFILE>` placeholders with the pipeline name and profile name in the following examples
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:warning: Remember to replace the `<PIPELINE>` and `<PROFILE>` placeholders with the pipeline name and profile name in the following examples
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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.
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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.
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