Tag: Nextflow

FONDA at SIGMOD

Mahdi Esmailoghli and Matthias Weidlich traveled to Bengaluru, India to participate in the SIGMOD 2026 conference. Mahdi presented his work on FlowPilot: A Suggestion System for Designing Scientific Workflows. FlowPilot extracts a variety of syntactic and semantic features from a corpus of existing scientific workflows to construct a similarity knowledge base. Using this knowledge base, FlowPilot can then suggest likely next steps to the user during workflow development.

FlowPilot outperforms state-of-the-art code-generating models such as Llama-4, and traditional methods, like association rule mining techniques on NextFlow workflows.

November 25th-26th: Workshop on reducing carbon emissions in large-scale computational data analysis

On Tuesday November 25th, in lieu of our normal Lecture Series talks, we will begin our Workshop on reducing carbon emissions in large-scale computational data analysis! The workshop will continue on Wednesday with more speakers and opportunities for discussion.

The workshop was planned in collaboration with the Quantitative Biology Center (QBiC), the bioinformatics core facility from the University of Tübingen. We have invited 14 speakers from around Europe and the UK to discuss current research into the environmental impacts of large scale scientific computing. More information, including the schedule, can be found here.

Data Aware Scheduling Method Now Available for Nextflow

With the latest release of the nf-cws Nextflow-Plugin, Fabian Lehmann and Friedrich Tschirpke introduce the WOW scheduling method as a production-ready feature. This release marks the transition of the WOW approach from a research prototype to a usable software component, fully integrated with the official Nextflow versions (v24.04.0 up to v25.02.3-edge).

Key Features:

  • WOW Scheduling for Nextflow: The Workflow-Aware data movement and task scheduling (WOW) method is now available as part of nf-cws. This enables dynamic coordination of data transfers and task execution, reducing network congestion and workflow runtime.
  • Seamless Integration: The nf-cws plugin can be used directly with Nextflow’s Kubernetes executor, requiring no experimental patches or custom setups.
  • Production Use: The improvements demonstrated in the original publication can now be leveraged by all Nextflow users in real-world scenarios.

-Fabian Lehmann

FONDA Integrated Research Training Group Courses

The Integrated Research Training Group (IRTG) has been very active in the past month providing courses and workshops for FONDA’s doctoral researchers. On April 28th and 29th Seqera, the company which supports the open source workflow engine “Nextflow” provided a tutorial using Nextflow to write and evaluate bioinformatics workflows. On May 7th, the IRTG members participated in a training course in Good Scientific Practice, especially geared towards computational sciences.

Future courses include a tutorial on GitLab with scientists from the German Aerospace Center on May 20th and 21st, a course on gender bias awareness on June 17, along with courses on workflow simulator WfCommons, and python-based workflow execution engine “Snakemake”.