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64 lines
5.1 KiB
Markdown
64 lines
5.1 KiB
Markdown
<img src="docs/images/nf-core-logo.png" width="400">
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# [nf-core/configs](https://github.com/nf-core/configs)
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[](https://travis-ci.org/nf-core/configs)
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[](https://codecov.io/gh/nf-core/configs)
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A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
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## Table of contents
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* [Using an existing config](#using-an-existing-config)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Adding a new config](#adding-a-new-config)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Help](#help)
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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.
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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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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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### Offline usage
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If you want to use an existing config available in `nf-core/configs`, and you're running on a system that has no internet connection, you'll need to download the config file and place it in a location that is visible to the file system on which you are running the pipeline. You can then run the pipeline with the `-c` parameter - see [Testing](#testing) for example.
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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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### Testing
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If you want to add a new custom config file to `nf-core/configs` please can you test that your pipeline of choice runs as expected by using the [`-c`](https://www.nextflow.io/docs/latest/config.html) parameter.
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```bash
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## Example command for nf-core/rnaseq
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nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]'
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```
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### Documentation
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You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the custom config file within your organisation.
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See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples.
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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` 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. 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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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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## Help
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If you have any questions or issues please send us a message on [Slack](https://nf-core-invite.herokuapp.com/).
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