Using nf-core resources outside nf-core

While we highly recommend and promote contributing to existing nf-core pipelines, in some cases this may not be possible or appropriate. In this case we hope that it will be helpful to use parts of nf-core best practices for your own non-nf-core pipeline. This tutorial describes how to use nf-core code without making official nf-core pipelines.

Acknowledging nf-core

If you use any form of nf-core code or infrastructure, we kindly ask that you acknowledge the nf-core initiative by adding the following markdown to your README.md and 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:

Removing nf-core only branding

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

General

  • Replace all 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 result in a lot of linting failures. You can create a .nf-core.yml file that allows you to ignore or skip certain lint tests. You can find more information on how to do this here. One example is the pipeline_name_conventions

README

To ensure users do not get confused, we suggest removing the following components of the main pipeline README:

  1. Remove (or replace) the nf-core logo (see below)

  2. Slack badge for help messages.

  3. Replace all references of the https://nf-co.re website to the location of your own documentation

  4. Remove reference to the nf-core Slack workspace under `Contributions and Support

  5. Replace the Citations section with the following markdown:

    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:

Optional:

  1. 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

docs/

  1. Replace the nf-core logo under docs/images with your own one.
    • You will also have to change the filename/path at the top the main repository README
  2. docs/usage.md: remove reference to documentation being viewable on the nf-co.re website
  3. docs/usage.md: remove reference to the nf-core Slack workspace

Optional:

  1. 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

.github/

  1. PULL_REQUEST_TEMPLATE.md: Remove reference to the nf-core/tests-datasets repository
  2. CONTRIBUTING.md: remove references to the nf-core Slack workspace
  3. workflows/: remove nf-core specific GitHub actions YAMLs
    • push_dockerhub*
  4. ci.yml: rename to the name of your pipeline rather than nf-core CI tests
  5. ISSUE_TEMPLATE/ Remove references to nf-core website in all templates and config files

Optional:

  1. CONTRIBUTING.md: remove references to the nf-core/tools linting tests
  2. workflows/: remove the nf-core linting tests under (Note: you can alternatively keep linting and configure to ignore certain tests)
    • linting.yml
    • linting_comment.yml
  3. workflows/: remove the AWS test GitHub action workflows
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