AI summaryⓘ
The authors studied nf-core, a community-maintained collection of scientific data pipelines, to understand how maintenance and user support happen across different platforms like GitHub and forums. They analyzed thousands of issues, pull requests, and forum discussions to see what kinds of problems come up and how they get fixed or answered. They found that GitHub issues mainly track bugs and coordination, pull requests handle code changes and testing, and forums focus on user help with running pipelines on various systems. Successful problem resolution often depends on clear information, assigned people, and good discussion. The authors also noticed that links between forum support and GitHub code are rare, showing these spaces are somewhat separate.
nf-coreNextflow pipelinesGitHub issuespull requestscommunity forumsoftware maintenanceuser supportdata-intensive researchworkflow automationrepository traceability
Authors
Khairul Alam, Kowsik Roy, Md Shamimur Rahman, Banani Roy
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.