Nextflow on Living Systems_

Setting up the Nextflow Language Server (LSP) with NeoVim

Fri, 16 May 2025 22:31:42 +0200

It turns out it is super easy to get Nextflow code intelligence to work in NeoVim now! This is thanks to the newly released Nextflow language server following the increasingly popular Language Server Protocol (LSP).

See this episode of the Nextflow podcast for a more in-depth discussion on this new functionality.

The focus has initially been on making this to work in the very popular Visual Studio Code editor, but through some recent developments by the community, setting it up in NeoVim is also pretty smooth.

Troubleshooting Nextflow pipelines

Wed, 01 Nov 2023 11:47:00 +0100

We have been evaluating Nextflow before in my work at pharmb.io , but that was before DSL2 and the support for re-usable modules (which was one reason we needed to develop our own tools to support our challenges, as explained in the paper ). Thus, there’s definitely some stuff to get into.

Based on my years in bioinformatics and data science, I’ve seen that the number one skill that you need to develop is to be able to effectively troubleshoot things, because things will invariably fail in all kinds of ways. And in the process, you will probably learn a lot about the technology stack you are using.

First production run with SciPipe - A Go-based scientific workflow tool

Thu, 28 Sep 2017 19:32:00 +0200

Today marked the day when we ran the very first production workflow with SciPipe , the Go -based scientific workflow tool we’ve been working on over the last couple of years. Yay! :)

This is how it looked (no fancy GUI or such yet, sorry):

The first result we got in this very very first job was a list of counts of ligands (chemical compounds) in the ExcapeDB dataset (download here ) interacting with the 44 protein/gene targets identified by Bowes et al as a good baseline set for identifying hazardous side-effects effects in the body (that is, any chemical compounds binding these proteins, will never become an approved drug).