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Merge pull request #225 from jfy133/doc-update
Make more explicit which files you must update
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0725e8d382
1 changed files with 12 additions and 5 deletions
17
README.md
17
README.md
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@ -63,7 +63,9 @@ 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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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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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.
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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.
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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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### Testing
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@ -134,11 +136,14 @@ Currently documentation is available for the following systems:
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### Uploading to `nf-core/configs`
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[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.
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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.
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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.
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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.
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Within the local clone of your fork:
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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:
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* **add** the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory
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* **add** the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory
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* **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
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* **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
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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:
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```bash
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Run python ${GITHUB_WORKSPACE}/bin/cchecker.py ${GITHUB_WORKSPACE}/nfcore_custom.config ${GITHUB_WORKSPACE}/.github/workflows/main.yml
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@ -157,6 +162,8 @@ 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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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 config, 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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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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