# Phil Ewels

> Personal website for Phil Ewels, a bioinformatician living in Stockholm, Sweden.

Phil Ewels is a software developer and bioinformatician in Stockholm, Sweden, working on
open-source tools for high-throughput genomics data. This site lists his work history,
software projects, conference talks and peer-reviewed publications.

Every page below is also available as Markdown by appending `.md` to its URL. The whole
site as a single document is at https://phil.ewels.co.uk/llms-full.txt.


## Profiles

- [GitHub](https://github.com/ewels/)
- [Bluesky](https://bsky.app/profile/ewels.bsky.social)
- [LinkedIn](http://uk.linkedin.com/in/philewels)
- [X (Twitter)](http://twitter.com/tallphil)
- [Mastodon](https://genomic.social/@ewels)
- [ORCiD](http://orcid.org/0000-0003-4101-2502)
- [Google Scholar](https://scholar.google.se/citations?user=KJt8R0kAAAAJ&view_op=list_works&sortby=pubdate)


## Work

- [Seqera](https://phil.ewels.co.uk/work/seqera.md): Seqera provides modern software engineering - for science. Built on a foundation of open-source tools, Seqera empowers organizations to solve more complex challenges, faster.
- [SciLifeLab](https://phil.ewels.co.uk/work/scilifelab.md): SciLifeLab is a centre for life sciences in Sweden. It's a collaboration between four Swedish universities (Stockholm Univeristy, Karolinska Institute, KTH, Uppsala University).
- [The Babraham Institute](https://phil.ewels.co.uk/work/babraham.md): The Babraham Institute is a life science research institute dedicated to making the fundamental discoveries needed to maintain health and improve wellbeing throughout life.
- [Wellcome Sanger Institute](https://phil.ewels.co.uk/work/sanger.md): During my undergraduate degree, I did a placement year at the Wellcome Sanger Institute: a research institute at the forefront of genomics research.


## Education

- [University of Cambridge](https://phil.ewels.co.uk/education/university_of_cambridge.md): I did my PhD and postdoc at the University of Cambridge, placed at the Babraham Institue. I was a member of Trinity Hall, one of the oldest colleges in Cambridge.
- [University of Bristol](https://phil.ewels.co.uk/education/university_of_bristol.md): I did my undergraduate studies at the University of Bristol, home to excellent teaching, research and a fantastic live-music scene.


## Projects


### Work projects

- [MultiQC](https://phil.ewels.co.uk/projects/multiqc.md): Aggregate results from bioinformatics analyses across many samples into a single report
- [nf-core](https://phil.ewels.co.uk/projects/nf-core.md): A community effort to collect a curated set of analysis pipelines built using Nextflow
- [Nextflow](https://phil.ewels.co.uk/projects/nextflow.md): Data-driven computational pipelines
- [RustQC](https://phil.ewels.co.uk/projects/rustqc.md): Fast genomics quality control tools for sequencing data, written in Rust
- [rewrites.bio](https://phil.ewels.co.uk/projects/rewrites-bio.md): A manifesto for AI-assisted modernisation of bioinformatics software
- [SRA Explorer](https://phil.ewels.co.uk/projects/sra_explorer.md): Mini web application to explore the NCBI SRA. Generates SRA/FastQ download URLs
- [nf-docs](https://phil.ewels.co.uk/projects/nf-docs.md): Generate beautiful API documentation for Nextflow pipelines

### Work projects (archived)

- [Cluster Flow](https://phil.ewels.co.uk/projects/clusterflow.md): A pipelining tool to automate and standardise bioinformatics analyses on cluster environments
- [Labrador](https://phil.ewels.co.uk/projects/labrador.md): A web based tool to manage and automate the processing of publicly available datasets

### Personal projects

- [Contributor Graphs](https://phil.ewels.co.uk/projects/contributor-graphs.md): A command-line tool that renders contributor timelines for any git or GitHub repository, as a publication-ready SVG and a self-contained interactive HTML page.
- [rich-click](https://phil.ewels.co.uk/projects/rich-click.md): Format click help output nicely with rich.
- [rich-codex](https://phil.ewels.co.uk/projects/rich-codex.md): Automatic terminal screenshots for documentation.
- [mkdocs-quiz](https://phil.ewels.co.uk/projects/mkdocs-quiz.md): Create interactive quizzes directly in your MkDocs markdown documentation.
- [starlight-quiz](https://phil.ewels.co.uk/projects/starlight-quiz.md): Create interactive quizzes directly in your Astro Starlight markdown documentation.
- [starlight-pydocs](https://phil.ewels.co.uk/projects/starlight-pydocs.md): Python API reference documentation for Astro Starlight sites.
- [gfm-tidy](https://phil.ewels.co.uk/projects/gfm-tidy.md): A userscript that adds buttons to GitHub's markdown toolbar, and lets you reorder or hide the rest.
- [Parking Alert](https://phil.ewels.co.uk/projects/parkingalert.md): Remember where your car is parked and get automated alerts when you need to move it.
- [Type Deck](https://phil.ewels.co.uk/projects/type-deck.md): A Stream Deck plugin that types preset text into the focused app, with optional human-like timing, typos, and jitter.
- [DeckCal](https://phil.ewels.co.uk/projects/deckcal.md): A Stream Deck plugin that turns a key into a live countdown to your next Google Calendar meeting, with a press to join it.
- [Pocket Money](https://phil.ewels.co.uk/projects/pocket-money.md): A family pocket money tracking app to help manage children's allowances and savings.


## Talks

- [scverse Conference 2026](https://phil.ewels.co.uk/talks/2026/10/12/scverse_conference.md): Invited keynote speaker at the third scverse conference, focused on single-cell and spatial data analysis
- [Bytesize: nf-core newsletter](https://phil.ewels.co.uk/talks/2026/06/23/bytesize_newsletter.md): Introducing the new monthly nf-core community newsletter
- [Webinar: What's new in Nextflow 26.04](https://phil.ewels.co.uk/talks/2026/06/17/whats_new_nextflow_26-04.md): Seqera Webinar with Ben Sherman about strict syntax, records, static typing and the new Module Registry
- [Nextflow Summit 2026 - Boston](https://phil.ewels.co.uk/talks/2026/04/30/nextflow_summit.md): Bioinformatics in the agentic age: Practical tips learnt from RustQC and rewrites.bio
- [The Bioinformatics CRO Webinar](https://phil.ewels.co.uk/talks/2026/02/18/the_bioinformatics_cro.md): Reproducible Bioinformatics at Scale: nf-core + Nextflow
- [Bytesize: Nextflow Plugin Registry](https://phil.ewels.co.uk/talks/2025/11/11/bytesize_plugin_registry.md): The why, the what and the how of the new Nextflow Plugin Registry
- [Nextflow Summit 2025](https://phil.ewels.co.uk/talks/2025/10/23/multiqc_nextflow_summit_2025.md): 10 years of MultiQC
- [ESS Max IV Summit 2025](https://phil.ewels.co.uk/talks/2025/10/03/ess_maxiv_summit.md): Invited panellist at the ESS / MAX IV / SciLifeLab Summit
- [Bytesize: RFCs](https://phil.ewels.co.uk/talks/2025/09/16/bytesize_rfcs.md): Introducing the new nf-core Request for Comment (RFC) process
- [EMBL Scientific Workflow Club](https://phil.ewels.co.uk/talks/2025/09/11/embl_workflows.md): Scaling standardisation in the nf-core community
- [European Space Agency: Living Planet Symposium](https://phil.ewels.co.uk/talks/2025/06/25/esa_living_planet.md): Nextflow in the stars ✨
- [Webinar: What's new - May 2025](https://phil.ewels.co.uk/talks/2025/05/27/whats_new_webinar.md): Recap of product announcements from the 2025 Boston Nextflow Summit
- [Scilifelab AI Seminar Series](https://phil.ewels.co.uk/talks/2025/05/23/scilifelab_ai_seminar_series.md): Formerly NBIS Artificial Intelligence and Integrative Omics Seminar Series
- [AI Engineering in Stockholm Meetup](https://phil.ewels.co.uk/talks/2025/04/23/ai_engineering_in_stockholm.md): Scientific workflows with LLMs and AI agents
- [SciLifeLab seminar: Automation of research processes with LLMs and AI](https://phil.ewels.co.uk/talks/2025/03/06/scilifelab_ai.md): Building and testing scientific workflows with LLMs and AI agents
- [Webinar: A new era for Nextflow](https://phil.ewels.co.uk/talks/2024/12/10/webinar_a_new_era_for_nextflow.md): Seqera Webinar with Ben Sherman about new Nextflow VS Code-driven development and syntax enhancements
- [Webinar: What's new - Autumn 2024](https://phil.ewels.co.uk/talks/2024/11/20/webinar_whats_new_-_autumn_2024.md): Recap of product announcements from the 2024 Barcelona Nextflow Summit
- [PyCon Sweden: Rich-click](https://phil.ewels.co.uk/talks/2024/11/14/pycon_sweden_rich-click.md): Accidentally popular: Beautiful CLI interfaces with rich-click
- [Swedish Bioinformatics Workshop 2024](https://phil.ewels.co.uk/talks/2024/11/05/sbw2024_keynote.md): From Bench to Big Data: What's new with MultiQC and Nextflow
- [Nextflow Summit 2024 Barcelona - MultiQC](https://phil.ewels.co.uk/talks/2024/10/31/nextflow_summit_2024_barcelona_-_multiqc.md): MultiQC: New features and flexible data parsing
- [Nextflow Summit 2024 Barcelona - nf-core Updates](https://phil.ewels.co.uk/talks/2024/10/31/nextflow_summit_2024_barcelona_-_nf-core_updates.md): Updates from the nf-core ecosystem
- [Bytesize: Excalidraw](https://phil.ewels.co.uk/talks/2024/09/17/bytesize_excalidraw.md): Intro to Excalidraw — a nifty tool for drawing diagrams.
- [Bytesize: Explaining Wave containers](https://phil.ewels.co.uk/talks/2024/06/11/bytesize_wave_containers.md): Build, upload, and manage container images using Wave
- [Bytesize: Get your containers with "Nextflow inspect"](https://phil.ewels.co.uk/talks/2024/05/28/bytesize_nextflow_inspect.md): Fetch all container URIs from a pipeline in one command
- [SciLifeLab Data Centre Retreat](https://phil.ewels.co.uk/talks/2024/04/23/scilifelab_data_centre_retreat.md): Invited speaker for the SciLifeLab DC group retreat
- [Bytesize: nf-core Special Interest Groups](https://phil.ewels.co.uk/talks/2024/02/20/bytesize_nf-core_special_interest_groups.md): Introducing a brand new nf-core initiative: Special Interest Groups.
- [Bytesize: Contributing to Nextflow](https://phil.ewels.co.uk/talks/2024/02/13/bytesize_nextflow_dev.md): Walkthrough of how to contribute code to Nextflow.
- [Oslo Bioinformatics Workshop Week 2023](https://phil.ewels.co.uk/talks/2023/12/14/oslo_bioinformatics_week.md): Nextflow and nf-core one day training event
- [Nextflow Summit Boston](https://phil.ewels.co.uk/talks/2023/11/29/nextflow_summit_boston_community_updates.md): Nextflow & nf-core community updates
- [Bytesize: The Art of a Minimal Example](https://phil.ewels.co.uk/talks/2023/11/14/bytesize_the_art_of_a_minimal_example.md): Part of the nf-core/bytesize series
- [Nextflow Summit Barcelona - MultiQC](https://phil.ewels.co.uk/talks/2023/10/20/nextflow_summit_2023_barcelona_multiqc.md): Bringing MultiQC into a new era
- [Nextflow Summit Barcelona - Community Updates](https://phil.ewels.co.uk/talks/2023/10/18/nextflow_summit_barcelona_community_updates.md): Nextflow & nf-core community updates
- [MDC/FMP Retreat 2023](https://phil.ewels.co.uk/talks/2023/08/28/mdc_retreat.md): Sponsor and speaker at the 2023 MDC/FMP PhD retreat
- [BIOMEDAS Retreat 2023](https://phil.ewels.co.uk/talks/2023/06/28/biomedas_retreat.md): Keynote speaker at the BIOMEDAS PhD retreat symposium.
- [Seqera Webinar: Nextflow best practices](https://phil.ewels.co.uk/talks/2023/06/21/seqera_nf-core_webinar.md): Leveraging nf-core tooling and standards within your organization.
- [IMN Presentation Skills Workshop](https://phil.ewels.co.uk/talks/2023/06/16/imn_visual_aids.md): "Visual Aids" training for PhD students and early stage researchers
- [Bytesize: Python packaging](https://phil.ewels.co.uk/talks/2023/05/02/bytesize_python_packaging.md): Converting Python scripts into packages for PyPI, Bioconda & Biocontainers
- [Bytesize: nf-core modules patch](https://phil.ewels.co.uk/talks/2023/03/07/bytesize_modules_patch.md): nf-core/bytesize talk about the patching functionality to modify shared modules
- [Genome Web webinar](https://phil.ewels.co.uk/talks/2022/12/15/genomeweb.md): Experiences with cloud compute in the nf-core open source community
- [Bytesize: Configuring lint tests](https://phil.ewels.co.uk/talks/2022/11/08/bytesize_configuring_lint_tests.md): nf-core/bytesize talk about the nf-core lint tests
- [Bytesize: GitHub via VSCode and CLI](https://phil.ewels.co.uk/talks/2022/11/29/bytesize_vscode_github.md): nf-core/bytesize talk showing how to work with GitHub using VSCode and Github CLI
- [BrazWebinars](https://phil.ewels.co.uk/talks/2022/11/25/brazwebinars.md): A series of webinars on Bioinformatics in Brazil
- [Open Box Science](https://phil.ewels.co.uk/talks/2022/11/15/open_box_science.md): A grassroots community organising free online talks and training
- [NextGenBug 2022](https://phil.ewels.co.uk/talks/2022/10/31/nextgenbug.md): Invited keynote speaker to the 2022 NextGen Bioinformatics User Group
- [Nextflow Summit 2022 - Hackathon report](https://phil.ewels.co.uk/talks/2022/10/14/summit_hackathon_summary.md): nf-core hackathon report
- [Nextflow Summit 2022 - Community updates](https://phil.ewels.co.uk/talks/2022/10/12/summit_community_updates.md): Community updates
- [Bytesize: Community updates ](https://phil.ewels.co.uk/talks/2022/09/27/bytesize_community_updates.md): nf-core community updates recap after the core team retreat
- [Karolinska Institute Seminar](https://phil.ewels.co.uk/talks/2022/06/20/karolinska_institute_huddinge.md): Educational seminar for the Centre for bioinformatics and biostatistics
- [CRG Nextflow course](https://phil.ewels.co.uk/talks/2022/06/06/crg_nextflow_course.md): BovReg Nextflow workshop organized by the CRG
- [Bytesize: 2022 Community Survey Results](https://phil.ewels.co.uk/talks/2022/05/23/bytesize_2022_community_survey_results.md): Summary of results from the Nextflow and nf-core 2022 community survey
- [Bytesize: Code linting tools](https://phil.ewels.co.uk/talks/2022/04/12/bytesize_code_linting_tools.md): Short talk about the different linting tools used in nf-core
- [Bytesize: Customising MultiQC Reports](https://phil.ewels.co.uk/talks/2022/03/08/bytesize_customising_multiqc_reports.md): nf-core/bytesize talk about lesser known MultiQC configuration options
- [Bytesize: Troubleshooting a failed pipeline](https://phil.ewels.co.uk/talks/2022/03/01/bytesize_debugging_pipeline_runs.md): A popular nf-core/bytesize talk about how to debug a failed Nextflow run
- [Genome Web webinar](https://phil.ewels.co.uk/talks/2021/12/01/genomeweb.md): Reproducible bioinformatics workflows with Nextflow and nf-core
- [NBIS Epigenomics course](https://phil.ewels.co.uk/talks/2021/10/28/nbis_epigenomics_course.md): Nextflow and nf-core
- [Swedish Bioinformatics Workshop](https://phil.ewels.co.uk/talks/2021/10/21/sbw.md): Reproducible bioinformatics workflows with Nextflow and nf-core


## Publications

- [Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds](https://phil.ewels.co.uk/publications/2026/osipova-science.md)
- [pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics](https://phil.ewels.co.uk/publications/2026/yue-molecular-and-cellular-proteomics.md)
- [Empowering bioinformatics communities with Nextflow and nf-core](https://phil.ewels.co.uk/publications/2025/langer-genome-biology.md)
- [A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines](https://phil.ewels.co.uk/publications/2025/chen-nature-methods.md)
- [Convergent and lineage-specific genomic changes contribute to adaptations in sugar-consuming birds](https://phil.ewels.co.uk/publications/2024/osipova-biorxiv.md)
- [Empowering bioinformatics communities with Nextflow and nf-core](https://phil.ewels.co.uk/publications/2024/langer-biorxiv.md)
- [A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements](https://phil.ewels.co.uk/publications/2023/arnqvist-g3-genes-genomes-genetics.md)
- [Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma](https://phil.ewels.co.uk/publications/2022/pena-perez-blood-advances.md)
- [Ten simple rules for making a software tool workflow-ready](https://phil.ewels.co.uk/publications/2022/brack-plos-computational-biology.md)
- [Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution](https://phil.ewels.co.uk/publications/2022/mueller-molecular-ecology.md)
- [DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics](https://phil.ewels.co.uk/publications/2021/bichmann-journal-of-proteome-research.md)
- [Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes](https://phil.ewels.co.uk/publications/2021/wojewodzic-clinical-epigenetics.md)
- [A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines](https://phil.ewels.co.uk/publications/2021/chen-biorxiv.md)
- [Linked-read sequencing enables haplotype-resolved resequencing at population scale](https://phil.ewels.co.uk/publications/2020/lutgen-molecular-ecology-resources.md)
- [Building an international consortium for tracking coronavirus health status](https://phil.ewels.co.uk/publications/2020/segal-nature-medicine.md)
- [The nf-core framework for community-curated bioinformatics pipelines](https://phil.ewels.co.uk/publications/2020/ewels-nature-biotechnology.md)
- [Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants](https://phil.ewels.co.uk/publications/2020/garcia-f1000research.md)
- [Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats](https://phil.ewels.co.uk/publications/2019/schweizer-molecular-phylogenetics-and-evolution.md)
- [nf-core: Community curated bioinformatics pipelines](https://phil.ewels.co.uk/publications/2019/ewels-biorxiv.md)
- [Cluster Flow: A user-friendly bioinformatics workflow tool](https://phil.ewels.co.uk/publications/2017/ewels-f1000research.md)
- [Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women](https://phil.ewels.co.uk/publications/2016/engstrom-archives-of-toxicology.md)
- [MultiQC: summarize analysis results for multiple tools and samples in a single report](https://phil.ewels.co.uk/publications/2016/ewels-bioinformatics.md)
- [Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression](https://phil.ewels.co.uk/publications/2016/ivanov-nucleic-acids-research.md)
- [A Complete Overhaul of the Electron Energy-Loss Spectroscopy and X-Ray Absorption Spectroscopy Database: eelsdb.eu](https://phil.ewels.co.uk/publications/2016/ewels-microscopy-and-microanalysis.md)
- [HiCUP: pipeline for mapping and processing Hi-C data](https://phil.ewels.co.uk/publications/2015/wingett-f1000research.md)
- [Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies](https://phil.ewels.co.uk/publications/2015/patalano-proceedings-of-the-national-academy-of-sciences.md)
- [Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C](https://phil.ewels.co.uk/publications/2015/mifsud-nature-genetics.md)
- [Global Reorganization of the Nuclear Landscape in Senescent Cells](https://phil.ewels.co.uk/publications/2015/chandra-cell-reports.md)
- [Understanding functional miRNA–target interactions in vivo by site-specific genome engineering](https://phil.ewels.co.uk/publications/2014/bassett-nature-communications.md)
- [Meet the neighbours: tools to dissect nuclear structure and function](https://phil.ewels.co.uk/publications/2011/osborne-briefings-in-functional-genomics.md)
- [Large Scale Association Analysis of Novel Genetic Loci for Coronary Artery Disease](https://phil.ewels.co.uk/publications/2009/arteriosclerosis-thrombosis-and-vascular-biology-2009.md)
- [Sorting nexin-1 defines an early phase of Salmonella-containing vacuole-remodeling during Salmonella infection](https://phil.ewels.co.uk/publications/2008/bujny-journal-of-cell-science.md)
- [High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia](https://phil.ewels.co.uk/publications/2008/baker-journal-of-clinical-microbiology.md)
- [Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease](https://phil.ewels.co.uk/publications/2008/fisher-nature-genetics.md)