From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics

Khairul Alam; Banani Roy

Home/Archive/arXiv

arXiv · 2507.20122

From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics

Khairul Alam·Banani Roy

View original source ↗Read source document ↗Export metadata ↓

Abstract

Scientific Workflow Systems such as Galaxy and Nextflow are essential for scalable, reproducible, and automated bioinformatics analyses. However, developing and understanding scientific workflows remains challenging for many domain scientists due to the complexity of tool/module selection, infrastructure requirements, and limited programming expertise. This study explores whether state-of-the-art Large Language Models such as GPT-4o, Gemini 2.5 Flash, and DeepSeek-V3 can assist in generating accurate, complete, and usable bioinformatics workflows. We evaluate a set of representative workflows covering tasks such as RNA-seq, SNP analysis, and DNA methylation across both Galaxy (graphical) and Nextflow (script-based) platforms. To simulate realistic usage, we adopt a tiered prompting strategy: each workflow is first generated using an instruction-only prompt; if the output is incomplete or incorrect, we escalate to a role-based prompt, and finally to chain-of-thought prompting if needed. The generated workflows are evaluated against community-curated baselines from the Galaxy Training Network and nf-core, using criteria including correctness, completeness, tool appropriateness, and executability. Results show that LLMs exhibit strong potential in workflow development. Gemini 2.5 Flash produced the most accurate and user-friendly workflows in Galaxy, while DeepSeek-V3 excelled in Nextflow pipeline generation. GPT-4o performed nicely with structured prompts. Prompting strategy significantly influenced output quality, with role-based and chain-of-thought prompts enhancing correctness and completeness. Overall, LLMs can reduce the cognitive and technical barriers to workflow development, making SWSs more accessible to novice and expert users. This work highlights the practical utility of LLMs and provides actionable insights for integrating them into real-world bioinformatics workflow design.

Explore related subjects

cs.SE

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Khairul Alam, Banani Roy. 2025-08-14. From Prompt to Pipeline: Large Language Models for Scientific Workflow Development in Bioinformatics. https://arxiv.org/abs/2507.20122

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

LLM-Based Repair of Static Nullability Errors

Modern Java projects increasingly adopt static analysis tools that prevent null-pointer exceptions by treating nullness as a type property. However, integrating such tools into large, existing codebases remains a significant challenge. While annotation inference can eliminate many errors automatically, a subset of residual errors $-$ typically a mix of real bugs and false positives $-$ often persists and can only be resolved via code changes. Manually addressing these errors is tedious and error-prone. Large language models (LLMs) offer a promising path toward automating these repairs, but naively prompted LLMs often generate incorrect, contextually inappropriate edits. We present NullRepair, a system that integrates LLMs into a structured workflow for resolving the errors from a nullability checker. NullRepair's decision process follows a flowchart derived from manual analysis of 200 real-world errors. It leverages static analysis to identify safe and unsafe usage regions of symbols, using error-free usage examples to contextualize model prompts. Patches are generated through an iterative interaction with the LLM that incorporates project-wide context and decision logic. Our evaluation on 12 real-world Java projects shows that NullRepair resolves 63% of the 1,119 nullability errors that remain after applying a state-of-the-art annotation inference technique. Unlike two baselines (single-shot prompt and mini-SWE-agent), NullRepair also largely preserves program semantics, with all unit tests passing in 10/12 projects after applying every edit proposed by NullRepair, and 98% or more tests passing in the remaining two projects.

cs.SE↗

arXiv2026

Metamodel-Guided Model Generation with Layered Constraints

Large language models (LLMs) enable natural-language interaction in engineering modeling, but generated models may violate structural constraints, domain rules, or task requirements. We propose a metamodel-guided model generation method that coordinates generation-time constraints and post-generation validation. The method transforms metamodel information, uses its terminology to guide structured constraint extraction from specifications, and links constraints to metamodel elements while recording their sources in an Integrated Constraint Model (ICM). For each task, relevant constraints are bound to concrete objects, values, and references. The generation-time constraint layer (L1) restricts candidate content. The post-generation validation layer (L2) checks constructed models and serialized artifacts, and task acceptance checks retain the original requirements throughout repair. Deterministic procedures construct and serialize models, while LLMs propose candidate content and repairs. Validation uses existing domain tools and checkers written by humans with LLM assistance. Experiments cover AUTOSAR, railway models, and structured decisions in private international law. All 60 AUTOSAR generation runs passed acceptance within the declared task scope, and all 255 resulting ARXML files passed XSD validation. In a separate controlled AUTOSAR repair experiment, all 85 core fault units and 15 prespecified substitute units were restored within one repair round. A local AUTOSAR experiment recorded interventions during stepwise generation. The results support coordinating generation constraints, domain checks, and task acceptance to construct models and guide bounded repair.

cs.SE↗

arXiv2026

VeriSoftBench: Repository-Scale Formal Verification Benchmarks for Lean

Large language models have achieved striking results in interactive theorem proving, particularly in Lean. However, most benchmarks for LLM-based proof automation are drawn from mathematics in the Mathlib ecosystem, whereas proofs in software verification are developed inside definition-rich codebases with substantial project-specific libraries. We introduce VeriSoftBench, a benchmark of 500 Lean 4 proof obligations drawn from open-source formal-methods developments and packaged to preserve realistic repository context and cross-file dependencies. Our evaluation of frontier LLMs and specialized provers yields three observations. First, provers tuned for Mathlib-style mathematics transfer poorly to this repository-centric setting. Second, success is strongly correlated with transitive repository dependence: tasks whose proofs draw on large, multi-hop dependency closures are less likely to be solved. Third, providing curated context restricted to a proof's dependency closure improves performance relative to exposing the full repository, but nevertheless leaves substantial room for improvement. Our benchmark and evaluation suite are released at https://github.com/utopia-group/VeriSoftBench.

cs.SE↗