millironx/nf-configs
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Merge pull request #225 from jfy133/doc-update

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Make more explicit which files you must update
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Phil Ewels 2021-11-19 00:56:50 +01:00 committed by GitHub
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@ -63,7 +63,9 @@ 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. Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](Using an existing config)), and then continuing with the next steps.
N.B. In your config file, 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.
### Testing ### Testing
@ -134,11 +136,14 @@ 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`](https://github.com/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:
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.
In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error: * **add** the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory
* **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory
* **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
* **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
In order to ensure that the config file is tested automatically with GitHub Actions please add your profile name to the `profile:` scope (under strategy matrix) in [`.github/workflows/main.yml`](.github/workflows/main.yml). If you forget to do this the tests will fail with the error:
```bash ```bash
Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
@ -157,6 +162,8 @@ 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 config, 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.