Short project summary

The NF-HELP project was initiated to support the NFDI4Microbiota consortium in strengthening workflow-based data analysis using Nextflow. During implementation, it became apparent that the originally planned approach, regular external expert drop-in sessions, did not meet a clearly articulated demand within the consortium. Direct outreach and open calls resulted in very limited interest. A follow-up consortium-wide survey provided more differentiated insights. While only a small number of participants requested individual support, the feedback revealed a preference for targeted, case-specific assistance rather than general expert sessions. Based on this evidence, the project strategy was adaptively reoriented to ensure effective use of Flex Funds and to maximize benefit for the consortium.

Individualized training and feedback were provided using internal expertise, avoiding
unnecessary external costs. The Flex Funds were instead strategically invested in the update and integration of an external workflow into the NFDI4Microbiota infrastructure via the Cloud-based Workflow Manager (CloWM). The integrated workflow is a modular ensemble taxonomic profiling pipeline designed for human stool and tissue microbiome analysis from whole-genome or whole-transcriptome sequencing data. It enables standardized quality control, host read removal, and microbial profiling using multiple established tools.

The workflow integration into CloWM was completed during the reporting period and resulted in a fully functional, reusable pipeline that is ready for deployment, pending final clarification of sensitive data requirements for the target CloWM instance. This activity delivers a concrete and sustainable contribution to NFDI4Microbiota and aligns with planned measures in the second funding phase, particularly those related to human-associated data and collaboration with GHGA.

Brief summary of the main results and conclusion

The NF-HELP flex fund successfully adapted to changing consortium needs and delivered a
concrete infrastructure contribution. While demand for general Nextflow training was limited, targeted internal support and the integration of a human-associated microbiome workflow into CloWM resulted in a reusable and strategically relevant outcome aligned with NFDI4Microbiota Phase 2 goals.