Mastodawn

"DBCLS BioHackathon 2025 report: Creation and Publication Analytical Workflow of Creators' Interests" https://doi.org/10.37044/osf.io/qd5sz_v1

"At the DBCLS BioHackathon 2025, we converted metatranscriptomic analytical shell scripts into Common Workflow Language (CWL) containerized with Docker. Sub-workflows were created for metagenomic assembly, read mapping, and gene annotation, and validated with test datasets. The workflows, released on GitHub and WorkflowHub, improve reproducibility and address issues of reusability and software environment dependency." https://index.biohackrxiv.org//2025/09/30/qd5sz.html

#WorkflowHub #biohackathon #BH25JP #CommonWorkflowLanguage

OSF

clacke: exhausted pixie dream boy 🇸🇪🇭🇰💙💛Sep 12, 2019

Running into issues with #AirFlow and sub-DAGs, and now I'm reading about #CommonWorkflowLanguage and #WorkflowDefinitionLanguage and wondering how they map onto #FlowBasedProgramming.

I'm having the same issue as Twine was having over at web.archive.org/web/2019091209… which I suppose I could solve the same kind of brute-force way they did, but it's easy to start diverging into more research.

I'm looking at Toil(0) and Arvados(0) and what they can do.

(0) toil.readthedocs.io/
(1) arvados.org/

I strongly suspect we'll end up just not running a workflow engine down the road. Our use case is not super complicated, but the workflow engine integration is turning out to be. The whole flow status monitoring UI *is* nice to have though.