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. We also evaluated CWL best practices from the perspective of life scientists, classifying them by difficulty, importance, and applicability to promote FAIR principles and software quality.In parallel, we established a benchmarking framework for pangenome-based structural variant (SV) calling using data from the Dai population. Graph-based references from the Human and Chinese Pangenome Consortia were compared with linear references using minimap2 and vg giraffe. Results showed improved alignment accuracy and variant detection with pangenomes, demonstrating their value for reducing mapping bias and enhancing SV discovery.
Mameda et al. (Tue,) studied this question.
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