I am writing a quarto .qmd document in RStudio and...
# helpr
Ramiro Barrantes Reynolds
12/19/2025, 4:05 PMI am writing a quarto .qmd document in RStudio and I would like to cite the nf-core pipeline that I used. What is the appropriate way to do that? I am using https://nf-co.re/seqinspector/dev/. I would cite nf-core of course, but in nf-core pipelines it usually says: An extensive list of references for the tools used by the pipeline can be found in the
CITATIONS.mdn
Niklas Schandry
12/20/2025, 5:41 PMI think all nfcore pipelines have a zenodo doi and are citeable. Personally i do not think that citing every tool cited by the pipeline is required, since we typically also do not cite all references found in a cited piece of literature.
Niklas Schandry
12/20/2025, 5:45 PMIt might make sense to cite specific tools that were important to the analysis, but i find it difficult to then draw a line on what not to cite..
j
James Fellows Yates
12/21/2025, 6:06 AMAs #C06PHJM0Y3D is not yet published it does not have a DOI.
James Fellows Yates
12/21/2025, 6:11 AMI disagree that you don't have to cite the tools in the pipeline too, as then it's unfair of the academic authors of those tools: they will not get citations, and thus can't prove funders it's a highly used tool and then cannot continue to develop it (or new tools). The exception to that is IMO if you use a pipeline that uses containers etc, you don't need the versions of every tool in a methods text, as they should be pinned against the pipeline version.
@novelvirus try running either #C031QH57DSS or #C062H82UCRG test profiles. You'll see towards the bottom of the MultiQC an auto generated methods text.
James Fellows Yates
12/21/2025, 6:15 AMFor example:
James Fellows Yates
12/21/2025, 6:15 AMFor #C062H82UCRG (a simple one)
James Fellows Yates
12/21/2025, 6:15 AMJames Fellows Yates
12/21/2025, 6:17 AM(Not all pipelines have this automatically generated text though)
s
Simon Pearce
12/23/2025, 10:15 AMI would say that any tool in the pipeline that you have used should be cited. If the pipeline includes a tool that you haven't used, I don't think you need to cite that (even if it is ran by default).
j
James Fellows Yates
12/23/2025, 10:47 AMExactly