Publication credit

All pipeline publications and presentations, or those that describe pipelines, should give attribution to the nf-core community.

All nf-core pipeline publications and presentations should cite The nf-core framework for community-curated bioinformatics pipelines:

Ewels, P.A., Peltzer, A., Fillinger, S. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38, 276–278 (2020). https://doi.org/10.1038/s41587-020-0439-x

At a minimum, the nf-core community should be thanked in the acknowledgment section. For example, the acknowledgement from the nf-core/clipseq) preprint:

We would also like to thank the nf-core team, in particular Harshil Patel, Phil Ewels and Maxime Garcia, for welcoming us to the nf-core community and their assistance in reviewing and releasing the pipeline. We would also like to thank the nf-core community for developing the nf-core infrastructure and resources for Nextflow pipelines. A full list of nf-core community members is available at https://nf-co.re/community.

Optionally, the nf-core community can be included as a consortium co-author. This option is preferred when a pipeline has made extensive use of existing nf-core pipeline components (e.g., modules and subworkflows) written by other community members who were not directly involved in the pipeline itself. For example, see hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.

If members of the nf-core community have provided significant input to the creation or maintenance of a pipeline, please consider adding them as coauthors on the pipeline publication or presentation.

We also strongly recommend transparency when working on a project where the pipeline plays a significant role. If you plan to write a paper about a pipeline, share this with the community in the pipeline-specific channel on the nf-core Slack workspace prior to and during the manuscript’s writing, and invite contributors to self-report their roles and discuss authorship expectations within the project group.

If your pipeline publication or presentation is an extension of a community pipeline, please discuss authorship with the main developers.

Determining fair guidelines for authorship in community-driven projects, especially those involving diverse contributors, can be challenging. Based on ICMJE’s recommendations for authorship, we suggest you evaluate the inclusion of contributors as co-authors based on the following four criteria:

- Substantial contributions to the conception or design of the pipeline; or the acquisition, analysis, or interpretation of data used to test/demo the pipeline; AND
- Drafting the work or reviewing it critically for important intellectual content; AND
- Final approval of the version to be published; AND
- Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

See Publications for more examples of nf-core and nf-core pipeline publications.