External use of nf-core resources

Whenever possible, you should contribute to existing nf-core pipelines. However, in some cases, this may not be possible or appropriate. In this case, you should still use parts of nf-core best practices for your own non-nf-core pipeline. This guide describes how to use nf-core code without making official nf-core pipelines.

If you use nf-core code or infrastructure for your own pipeline development, you must acknowledge the nf-core initiative and follow these guidelines for proper attribution and branding.

Acknowledge nf-core

When using nf-core code or infrastructure, include this acknowledgment in your pipeline documentation:

This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
 
> The nf-core framework for community-curated bioinformatics pipelines.
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
> In addition, references of tools and data used in this pipeline are as follows:

Remove nf-core branding

Most of the following suggestions refer to when you have started your pipeline using the nf-core template.

General

Replace the following:

  • References to the pipeline name that include the nf-core/ suffix.

    Warning

    If you still wish to use the nf-core tools linting functionality, this may cause linting failures.

Create a .nf-core.yml file that allows you to ignore or skip certain lint tests. See linting config for more information. :::

README

Remove the following:

  • The nf-core logo

  • Slack badge for help messages

  • References to the https://nf-co.re website

  • References to the nf-core Slack workspace

  • (Optional) Reference to nf-core/configs in Quick Start

    Note

    In many cases it is still reasonable to use these configs for non-nf-core pipelines as they typically only modify generic Nextflow options.

Replace the following:

  • The Citations section with the following:
This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) initative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).
 
> The nf-core framework for community-curated bioinformatics pipelines.
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
 
In addition, references of tools and data used in this pipeline are as follows:

docs/

Remove the following:

  • docs/usage.md: Reference to documentation being viewable on the nf-co.re website

  • docs/usage.md: Reference to the nf-core Slack workspace

  • (Optional) Reference to nf-core/configs in -profile

    Note

    In many cases it is still reasonable to use these configs for non-nf-core pipelines as they typically only modify generic Nextflow options.

Replace the following:

  • The nf-core logo under docs/images

    Note

    You will also have to change the filename/path at the top the main repository README

.github/

Remove the following:

  • PULL_REQUEST_TEMPLATE.md: Reference to the nf-core/tests-datasets repository
  • CONTRIBUTING.md: References to the nf-core Slack workspace
  • CONTRIBUTING.md: (Optional) References to the nf-core/tools linting tests
  • workflows/: nf-core specific GitHub actions YAMLs
    • push_dockerhub*
  • workflows/: (Optional) nf-core linting tests under (Note: you can alternatively keep linting and configure to ignore certain tests)
    • linting.yml
    • linting_comment.yml
  • workflows/: (Optiona) AWS test GitHub action workflows
  • ISSUE_TEMPLATE/ Remove references to nf-core website in all templates and config files

Rename the following:

  • ci.yml: The name of your pipeline (rather than nf-core CI tests)
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