Maintenance and Support in Community-Driven Scientific Pipeline Ecosystems: A Cross-Platform Empirical Study of nf-core

Abstract

Community-driven scientific pipeline ecosystems are increasingly important for reproducible data-intensive research, but their sustainability depends on more than workflow engines, templates, and testing infrastructure. It also depends on how communities maintain pipelines, integrate contributions, and support users across heterogeneous execution environments. This paper presents a cross-platform empirical study of maintenance and support in nf-core, a large ecosystem of standardized Nextflow pipelines. We analyze 15,760 GitHub issues, 35,411 GitHub pull requests, and 895 Seqera Community Forum discussions to examine what maintenance and support concerns arise, how they differ across artifact types, which factors are associated with resolution outcomes, and how problems and solutions flow between repository-centered and community-centered spaces. We find that issues primarily capture repository-level problem reporting and maintenance coordination; pull requests capture implementation, review, testing, dependency, and template-update work; and forum discussions capture user-facing support around execution failures, containers, cloud and HPC environments, MultiQC reporting, and Nextflow usage. Resolution outcomes are associated with actionability, coordination, and diagnostic evidence. Issue closure is linked to assignees, comments, milestones, bug labels, error mentions, and version information. Pull request integration varies by author role, automation type, draft status, checklists, linked issues, and review routing. Forum accepted answers are more likely when discussions include code blocks, sustained interaction, and concrete technical evidence, while cloud, HPC, and workflow-semantics questions are harder to resolve. Cross-platform analysis reveals strong repository-internal traceability within GitHub, but limited explicit linkage between forum discussions and repository artifacts.