Intuitive Graphical Interface for Executing nf-core Pipelines

Question

[Nour-eddine]

I'm interested in developing an web application with a graphical user interface (GUI) to streamline the use of nf-core pipelines(sarek) for biologists. The goal is to create a user-friendly tool that would allow users to easily specify analysis parameters, manage input and output data, and track the progress of analyses, all without needing to use the command line or master technical aspects of computing. If you have ideas on how to design and develop such an application, or if you have practical advice for approaching this project, I would greatly appreciate hearing them. Thanks in advance for your help!

[Pierre Lindenbaum]

change your title to english please.

Answer 1

[pbioinf]

NF-core already has this functionality. You can start a run on the commandline and get served a link to a website where you can fill out all parameters. If you need even more user-friendly methods you can use nextflow-tower, which has free and paid tiers depending on how intensively you will use it.

Why is the title in French?

[Nour-eddine]

Thank you for the information about NF-core and Nextflow Tower. I appreciate the suggestion.

Regarding the title, I have changed it to English for clarity.

Answer 2

[Matthias Zepper]

The developers of Nextflow already offer such a solution called Seqera Platform (formerly Nextflow Tower). There are various commercial competitors like Pluto.bio, Form Bio, Gencove, Lifebit NF-Copilot, Latch.bio and many more, but they serve mostly the pharmaceutical industry. Academic users can buy licenses, of course, but grad student hours are cheap, so they usually don't ;-)

I suggest you find an open-source project that you can contribute to. nf-shard comes to my mind specifically, but sapporo is also interesting, because it is an open-source platform like the one you are looking to build and is also not restricted to Nextflow, but also supports e.g. Snakemake.

If you prefer to build your own, I suggest writing a frontend application that interacts with the official Seqera agent. This agent is the one used by Seqera platform to interact with on-premise clusters (e.g. running Slurm and Apptainer) and the API documentation is open. You could e.g. use Elysia to make the requests directly from Typescript.

[Nour-eddine]

Thank you for the detailed suggestions and information. I am particularly interested in your recommendation about building my own solution by writing a frontend application that interacts with the official Seqera agent.

[Matthias Zepper]

Great! There is a dedicated post category "Share a tool" in this forum, so once you have a working prototype, people will certainly be happy to learn about it and try it out. I am definitively curious what you will build, since I think such an undertaking is too complex for a single developer, but I do not know your skills and experience and thus might be too pessimistic. Good luck!