nf-core/configs

A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.

Table of contents

• Using an existing config
  • Configuration and parameters
  • Offline usage
• Adding a new config
  • Testing
  • Documentation
  • Uploading to nf-core/configs
• Help

Using an existing config

The Nextflow -c 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 for examples.

Configuration and parameters

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.

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 on your HPC you can add and customise the Nextflow Singularity scope to your config file. Similarly, you can add and customise a Nextflow executor 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.

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.

Offline usage

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 for example.

Adding a new config

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 for examples.

Testing

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 parameter.

## Example command for nf-core/rnaseq
nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -c '[path to custom config]'

Documentation

You will have to create a Markdown document outlining the details required to use the custom config file within your organisation.

See nf-core/configs/docs for examples.

Uploading to nf-core/configs

Fork 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/ directory, and the documentation file to the docs/ directory. You will also need to edit and add your custom profile to the nfcore_custom.config file in the top-level directory of the clone.

Commit and push these changes to your local clone on GitHub, and then create a pull request on the nf-core/configs GitHub repo with the appropriate information.

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.

Help

If you have any questions or issues please send us a message on Slack.