millironx/nf-configs
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A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions. A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
## Table of contents ## Table of contents
* [Introduction](#introduction)
* [Overview](#overview) * [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config)
* [Testing](#testing) * [Testing](#testing)
* [Documentation](#documentation) * [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) * [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Help](#help) * [Help](#help)
## Overview ## Introduction
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 create a custom config file that defines some generic settings unique to the computing environment within your organisation. 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. 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 create a custom config file that defines some generic settings unique to the computing environment within your organisation. 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. See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
## Testing ## Using an existing config
### Configuration and parameters
### Offline usage
## Adding a new config
### Testing
Once you have created your custom config file 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. Once you have created your custom config file 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.
@ -29,13 +41,13 @@ Once you have created your custom config file please can you test that your pipe
nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]' nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]'
``` ```
## Documentation ### Documentation
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. 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.
See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples. See [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs) for examples.
## Uploading to `nf-core/configs` ### Uploading to `nf-core/configs`
[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. [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.