Patrick Hüther
Bioinformatician
Vienna, Austria
Summary
🤩
Rockstar🎓
Top SchoolPatrick Hüther is a bioinformatician with 13 years of experience building reproducible genomics pipelines and production-ready tooling, currently based in Vienna and working at the Institute of Molecular Biology. He combines a strong academic background (PhD in Molecular Biology) with hands-on DevOps and backend engineering, contributing to high-profile open-source projects like Nextflow and the nf-core ecosystem. His contributions span module development, test automation, and container integrations (including Charliecloud support), reflecting a focus on robust, portable bioinformatics workflows. Patrick has driven reproducibility improvements in methylation and bisulfite-seq pipelines and automated environment and release processes to reduce deployment drift. Colleagues rely on him to bridge biological insight and software engineering, turning complex analysis steps into deterministic, testable components. He often improves infrastructure in subtle ways—like deterministic reporting and environment-export validation—that significantly raise long-term pipeline reliability.
13 years of coding experience
2 years of employment as a software developer
Doctor of Philosophy - PhD, Molecular Biology, pass with distinction, Doctor of Philosophy - PhD, Molecular Biology, pass with distinction at Universität WienDipl.-Biochem., Biochemistry, very good, Dipl.-Biochem., Biochemistry, very good at University of TübingenDAAD ISAP Fellowship, DAAD ISAP Fellowship at Capital Normal UniversityHigh School Diploma, High School Diploma at Leibniz Gymnasium Pirmasens
German, English
Github Skills (30)
go-modules10
docker10
python10
dsl10
workflow-engine10
kernel-module10
dockers10
nextflow10
pipeline-framework10
automation10
pipeline10
yaml10
bioinformatics10
jsmodules10
automations10
Programming languages (14)
Github contributions (5)
nf-core/methylseq
Nov 2018 - May 2021
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Role in this project:
Back-end Developer
Back-end DeveloperContributions:1 release, 25 reviews, 189 commits in 2 years 5 months
Contributions summary:Patrick's contributions primarily involve modifying and improving the Bismark methylation analysis pipeline. They focused on making the Bismark report deterministic, refactoring and enhancing the bwameth and bismark alignment steps, and implementing a mechanism to identify samples by name within the pipeline. The commits also include adding essential file management tools such as "where_are_my_files.txt". They fixed a bug that occurred when running bismark alignment with the --unmapped flag.
nf-coreanalysis-pipelinepipelinebisulfite-sequencingdna-methylation
nf-core/tools
Apr 2019 - Mar 2021
Python package with helper tools for the nf-core community.
Role in this project:Automation Engineer / Build & Release Engineer
Automation Engineer / Build & Release EngineerContributions:9 reviews, 29 commits, 11 PRs in 1 year 11 months
Contributions summary:Patrick primarily focused on improving the build and testing processes for the nf-core/tools project. Their contributions involved modifying scripts to bump pipeline versions, particularly within `environment.yml` and Dockerfiles, and introducing automated tests to validate conda environment exports. They also updated the testing framework to better reflect expected failures, ensuring robust quality control.
nf-corelinterpythonpipelinelinting
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