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README.md
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README.md
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## Using an existing config
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The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
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The Nextflow [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter can be used with nf-core pipelines in order to load custom config files that you have available locally. However, if you or other people within your organisation are likely to be running nf-core pipelines regularly it may be a good idea to use/create a custom config file that defines some generic settings unique to the computing environment within your organisation.
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### Configuration and parameters
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The config files hosted in this repository define a set of parameters which are specific to compute environments at different Institutions but generic enough to be used with all `nf-core` pipelines.
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The config files hosted in this repository define a set of parameters which are specific to compute environments at different Institutions but generic enough to be used with all nf-core pipelines.
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All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customise the [`Nextflow Singularity scope`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) to your config file. Similarly, you can add and customise a [`Nextflow executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are available to nf-core pipelines.
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All nf-core pipelines inherit the functionality provided by Nextflow, and as such custom config files can contain parameters/definitions that are available to both. For example, if you have the ability to use [Singularity](https://singularity.lbl.gov/) on your HPC you can add and customise the Nextflow [`singularity`](https://www.nextflow.io/docs/latest/config.html#scope-singularity) scope in your config file. Similarly, you can define a Nextflow [`executor`](https://www.nextflow.io/docs/latest/executor.html) depending on the job submission process available on your cluster. In contrast, the `params` section in your custom config file will typically define parameters that are specific to nf-core pipelines.
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You should be able to get a good idea as to how other people are customising the execution of their nf-core pipelines by looking at some of the config files in [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf).
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## Adding a new config
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If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all `nf-core` pipelines, and to everyone within your organisation. 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.
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If you decide to upload your custom config file to `nf-core/configs` then this will ensure that your custom config file will be automatically downloaded, and available at run-time to all nf-core pipelines, and to everyone within your organisation. 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.
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### Testing
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Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
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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.
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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.
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## Help
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