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Merge pull request #308 from maxulysse/refactor
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‎.github/workflows/build-cv.yml‎

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name: build-cv
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on:
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push:
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branches:
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- main
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paths:
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- src/data/CV-MGarcia.tex
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- src/data/biblio.bib
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jobs:
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build-cv:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Java
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uses: actions/setup-java@v4
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with:
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distribution: temurin
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java-version: "17"
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- name: Set up Nextflow
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uses: nf-core/setup-nextflow@v2
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with:
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version: "25.10.4"
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- name: Compile latest CV
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run: nextflow run maxulysse/compile-latex -r 3.0.1 -profile docker --outdir . --github_avatar 'https://avatars.githubusercontent.com/u/1019628?s=300&v=4' --input src/data/CV-MGarcia.tex --outname CV-MGarcia-latest.pdf --biblio src/data/biblio.bib
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- name: Commit and push to cv branch
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if: github.event_name == 'push' && github.ref == 'refs/heads/main'
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run: |
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git config --local user.email "action@github.com"
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git config --local user.name "GitHub Action"
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git checkout -B cv
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git add -f CV-MGarcia-latest.pdf
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git commit -m "Update CV - $(date +%Y-%m-%d)"
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git push -f origin cv

‎.gitignore‎

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.env
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.env.local
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.env.*.local
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# Nextflow CV
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.nextflow*
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pipeline_info/
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work/
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*.pdf

‎package-lock.json‎

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‎package.json‎

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},
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"dependencies": {
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"@astrojs/rss": "^4.0.18",
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"@orcid/bibtex-parse-js": "^0.0.25",
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"astro": "^6.1.6"
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},
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"devDependencies": {

‎src/content.config.ts‎

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import { defineCollection, z } from "astro:content";
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import { defineCollection } from "astro:content";
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import { glob } from "astro/loaders";
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import { z } from "zod";
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const blogCollection = defineCollection({
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loader: glob({ pattern: "**/*.{md,mdx}", base: "./src/content/blog" }),

‎src/data/CV-MGarcia.tex‎

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%!TEX program = xelatex
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% Made with modernCV: https://github.com/xdanaux/moderncv
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% moderncv definition
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\documentclass[11pt,a4paper,sans]{moderncv}
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\definecolor{color1}{RGB}{0,0,139}
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\moderncvstyle{classic}
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% Manage page size
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\RequirePackage[scale=0.9]{geometry}
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% Manage encoding
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\RequirePackage[utf8]{inputenc}
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\RequirePackage[english]{babel}
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% Good bibliography
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\RequirePackage[backend=biber, doi=true, sorting=ydnt]{biblatex}
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\addbibresource[datatype=bibtex]{biblio.bib}
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\RequirePackage{csquotes}
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% Nice and fancy font-icons
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\RequirePackage{academicons}
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\RequirePackage{fontawesome5}
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\RequirePackage{fontspec}
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% Nice and fancy underlines
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\RequirePackage[normalem]{ulem}
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\RequirePackage{contour}
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\renewcommand{\ULdepth}{1.8pt}\contourlength{0.6pt}
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\newcommand{\myuline}[1]{\uline{\contour{white}{#1}}}
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\newcommand{\myurl}[1]{\myuline{\url{{#1}}}}
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\newcommand{\mycomment}[1]{\cvitem{}{\small{#1}}}
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\newcommand{\mycvitemcomment}[3]{\cvitem{\faCalendar\hfill{#1}}{{#2}\hfill\small{#3}}}
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\newcommand{\mycvitemEDU}[5]{\cvitem{\faCalendar\hfill{#1}}{\textbf{#2}, \textit{#3}, {#4}\hfill\faMapMarker\ {#5}}}
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\newcommand{\mycvitemPP}[3]{\cvitem{\faCalendar\hfill{#1}}{{#2}\hfill\faMapMarker\ {#3}}}
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\newcommand{\mycvitemXP}[4]{\cvitem{\faCalendar\hfill{#1}}{\textbf{#2}, \textit{#3}\hfill\faMapMarker\ {#4}}}
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% Author information
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% Name
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\name{Maxime}{Garcia}
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% Title
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\title{PhD in Bioinformatics}
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\extrainfo{
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% Date of birth
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\faCalendar\ 1982-05-14\\
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% Phone number
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\faMobile\ +46-(0)7-237-343-36\\
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% % Twitter
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% \faTwitter\ \myuline{\href{https://twitter.com/gau/}{\nolinkurl{@gau}}}\\
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% Github
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\faGithub\ \myuline{\href{https://github.com/maxulysse/}{\nolinkurl{@maxulysse}}}\\
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% Email
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\faEnvelope\ \myuline{\href{mailto:maxime.garcia@scilifelab.se}{\nolinkurl{maxime.garcia@scilifelab.se}}}\\
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% Website
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\faGlobeEurope\ \myurl{https://maxulysse.github.io/}
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}
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% Picture
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\photo[64pt][2pt]{github_avatar}
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% Quote
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\quote{Automation, analysis, reproducibility and visualization}
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\begin{document}
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\makecvtitle
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\section{\texorpdfstring{\faBuilding\ Experience}{Experience}}
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\mycvitemXP{From 2025}{Bioinformatician}{NGI | ScilifeLab}{Stockholm, Sweden}
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\mycomment{Analysis; Data delivery; Infrastructure deployment.}
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\mycomment{Pipeline development; Community management; Community outreach. (\faGithub\ \myuline{\href{https://github.com/nf-core}{\nolinkurl{nf-core}}})}
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\mycvitemXP{2022--2025}{Bioinformatician}{Scientific Development | Seqera Labs}{Barcelona, Spain}
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\mycomment{Pipeline development; Community management; Community outreach. (\faGithub\ \myuline{\href{https://github.com/nf-core}{\nolinkurl{nf-core}}})}
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\mycvitemXP{2016--2022}{Bioinformatician}{Barntumörbanken | Karolinska Institutet \& NGI | ScilifeLab}{Stockholm, Sweden}
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\mycomment{Whole Genome/Targeted Sequencing Germline/Somatic analysis (\faGithub\ \myuline{\href{https://github.com/nf-core/sarek}{\nolinkurl{nf-core/sarek}}});}
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\mycomment{RNA-seq analysis (\faGithub\ \myuline{\href{https://github.com/nf-core/rnafusion}{\nolinkurl{nf-core/rnafusion}}} - \faGithub\ \myuline{\href{https://github.com/nf-core/rnavar}{\nolinkurl{nf-core/rnavar}}});}
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\mycomment{Community management. (\faGithub\ \myuline{\href{https://github.com/nf-core}{\nolinkurl{nf-core}}})}
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\mycvitemXP{2013--2014}{Research Associate}{Cancer Science Institute of Singapore (CSI)}{Singapore, Singapore}
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\mycomment{RNAseq analysis; Genome Browser Development.}
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\mycvitemXP{2009--2013}{PhD candidate}{Centre de Recherche en Cancérologie de Marseille (CRCM)}{Marseille, France}
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\mycomment{Development of an Interactome-Transcriptome analysis pipeline; Intern management.}
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\vfill
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\section{\texorpdfstring{\faUniversity\ Education}{Education}}
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\mycvitemEDU{2013}{PhD}{Bioinformatics and Genomics}{Aix-Marseille Université}{Marseille, France}
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\mycvitemEDU{2007--2009}{Master's Degree}{Bioinformatics and Genomics}{Université Aix-Marseille II}{Marseille, France}
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\mycvitemEDU{2007}{Erasmus Semester}{School of Biological Sciences}{University of East Anglia}{Norwich, UK}
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\mycvitemEDU{2003-2007}{Bachelor's Degree}{Biology and Biochemistry}{Université Aix-Marseille II}{Marseille, France}
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\vfill
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\nocite{*}
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\section{\texorpdfstring{\faBook\ Selected Publications}{Selected Publications}}
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\printbibliography[heading=none]
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% \printbibliography[type=article,heading=subbibliography,title={Articles}]
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% \printbibliography[type=inbook,heading=subbibliography,title={Chapters}]
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\vfill
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\section{\texorpdfstring{\faLaptop\ Skills}{Skills}}
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\cvdoubleitem{Scripting}{Groovy, Bash, R}{Pipeline}{Nextflow}
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\cvdoubleitem{reproducibility}{Docker, Bioconda, Apptainer}{Management}{GitHub, Jira, Slack}
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\cvdoubleitem{Web}{Astro}{+}{HTML5, CSS3, SASS, JS}
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\cvdoubleitem{Others}{Inkscape, \LaTeX, Workadventure}{+}{Linux, Clusters, Git, CI}
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\clearpage
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\vfill
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\section{\texorpdfstring{\faComments\ Selected Presentations}{Selected Presentations}}
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\mycvitemPP{2024}{24ème Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM)}{Toulouse, France}
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\mycvitemPP{2023}{Nextflow Summit}{Boston, USA}
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\mycvitemPP{2023}{Nextflow Summit}{Barcelona, Spain}
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\mycvitemPP{2020}{20ème Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM)}{Montpellier, France}
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\mycvitemPP{2019}{4th Scandinavian Seminar on Translational Pathology}{Bergen, Norway}
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\mycvitemPP{2018}{FoUU-day for clinical pathology-cytology}{Stockholm, Sweden}
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\mycvitemPP{2018}{19ème Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM)}{Marseille, France}
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\mycvitemPP{2018}{SPHN Workflow Interoperability Workshop}{Basel, Switzerland}
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% \mycvitemPP{2011}{Mathematical and Statistical Aspects of Molecular Biology XXI}{Vienna, Austria}
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\mycvitemPP{2010}{Cancer Bioinformatics Workshop}{Cambridge, UK}
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\vfill
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\section{\texorpdfstring{\faFileImage\ Selected Posters}{Selected Posters}}
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\mycvitemPP{2025}{Nextflow Summit}{Boston, USA}
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\mycvitemPP{2018}{Keystone Symposia Precision Medicine in Cancer}{Stockholm, Sweden}
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\mycvitemPP{2018}{Frontiers in Cancer Research and Therapy 2018}{Stockholm, Sweden}
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% \mycvitemPP{2017}{Department of Oncology-Pathology Kick Off}{Stockholm, Sweden}
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\mycvitemPP{2017}{European Human Genetics Conference (ESHG)}{Copenhagen, Denmark}
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% \mycvitemPP{2017}{Frontiers in Cancer Research and Therapy 2017}{Stockholm, Sweden}
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\mycvitemPP{2016}{The XVth KI Cancer Retreat}{Djurö, Sweden}
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% \mycvitemPP{2013}{5th Frontiers in Cancer Science (FCS)}{Singapore, Singapore}
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\mycvitemPP{2012}{11th European Conference on Computational Biology (ECCB)}{Basel, Switzerland}
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\mycvitemPP{2012}{13ème Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM)}{Rennes, France}
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% \mycvitemPP{2012}{6ème Colloque du Cancéropôle PACA}{Marseille, France}
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\mycvitemPP{2011}{12ème Journées Ouvertes en Biologie Informatique et Mathématiques (JOBIM)}{Paris, France}
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% \mycvitemPP{2011}{19th meeting of doctoral school}{Marseille, France}
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% \mycvitemPP{2010}{Biologistes Chimistes et Physiciens VII}{Marseille, France}
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% \mycvitemPP{2010}{Interactomics: at the crossroads of biology and bioinformatics}{St Raphaël, France}
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\vfill
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% \section{\texorpdfstring{\faUniversity\ Fellowhips}{Fellowhips}}
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% \mycvitemcomment{2012}{ECCB’12 Conference Fellowship from SIB Swiss Institute of Bioinformatics}{}
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% \mycvitemcomment{2011}{Travel grant from MASAMB organisation}{}
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% \mycvitemcomment{2009}{PhD fellowhip from INSERM/Région PACA}{}
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% \vfill
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\section{\texorpdfstring{\faList\ Organization and Events}{Organization and Events}}
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\mycvitemcomment{From 2018}{nf-core/hackathon}{(Member of organization committee)}
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\mycvitemcomment{2015}{Journées nationales de la CFD}{(Member of organization committee and Webmaster)}
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\mycvitemcomment{2012}{Doctoriales en Provence}{(Member of organization committee)}
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\mycvitemcomment{2011}{Marché de la Chimie - Fête de la Science}{(Conception and Animation of a stand)}
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\mycvitemcomment{2011}{7th BIOTechno forum in Marseille}{(Head of organization committee)}
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\mycvitemcomment{2009-2012}{Annual meeting of doctoral school in Biology and Health Sciences from Aix-Marseille University}{}
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\mycomment{\hfill(Member of organization committee)}
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\mycvitemcomment{2007-2011\hfill}{Plan de Cuques French Comics Festival}{(Logistic support)}
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\vfill
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\section{\texorpdfstring{\faUsers\ Associations}{Associations}}
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\mycvitemcomment{2012-2019}{Contributor to \faGlobeEurope\ \myurl{http://bioinfo-fr.net/}}{(Collaborative French-speaking bioinformatics blog)}
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\mycvitemcomment{2012-2014}{Vice-president of JeBiF - RSG-France}{(Association of French Young Bioinformaticians)}
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\mycvitemcomment{2010-2011}{President of Hippo'Thèse}{(Association of young researchers in Biology at Aix-Marseille University)}
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\mycvitemcomment{2010-2011}{Vice-president \&\ Webmaster of BIOTechno Network}{}
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\mycomment{\hfill(French Network of Associations organizing forums about careers in Biotechnology)}
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\mycvitemcomment{2009-2010}{Webmaster of Hippo'Thèse}{}
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\vfill
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% \section{Scientific Societies}
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% \cvitem{BioinfoDiag}{Member of Réseau Français de Bioinformatique pour le Diagnostic}
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% \cvitem{ISCB}{Member of International Society of Computational Biology}
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% \cvitem{SFBI}{Member of Société Française de BioInformatique}
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% \cvitem{CFD}{Member of Communauté Française des Docteurs}
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% \vfill
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\section{\texorpdfstring{\faComment\ Languages}{Languages}}
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\cvitem{French}{Native\hfill\ English Fluent\hfill\ Swedish Notions}
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\vfill
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\section{\texorpdfstring{\faInfoCircle\ Interests}{Interests}}
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\cvitem{}{Yoga, Cinema, Board-Games, Gardening, Video-Games, Science-Fiction, Popular science}
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\end{document}

‎src/data/biblio.bib‎

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@article{garcia2020sarekf1000,
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author = {Garcia, Maxime U. and Juhos, Sandor and Larsson, Malin and Olason, Palmi I. and Martin, Marcel and Eisfeldt, Jonas and DiLorenzo, Silvia and Sandgren, Stefan and Diaz de Stahl, Theresa and Ewels, Philip and Wirta, Ville and Nister, Mats and Kaller, Max and Nystedt, Bjorn},
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title = {Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]},
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journal = {F1000Research},
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year = {2020},
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volume = {9},
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pages = {63},
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doi = {10.12688/F1000RESEARCH.16665.2},
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pubmed = {32269765},
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section = {articles}
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}
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@article{ewels2020nfcore,
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author = {Ewels, Philip and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime U. and Di Tommaso, Paolo and Nahnsen, Sven},
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title = {The nf-core framework for community-curated bioinformatics pipelines},
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journal = {Nature Biotechnology},
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year = {2020},
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doi = {10.1038/s41587-020-0439-x},
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pubmed = {32055031},
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section = {correspondences}
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}
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@article{fellowsyates2021eager,
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author = {Fellows Yates, James A. and Lamnidis, Thiseas C. and Borry, Maxime and Valtuena, Andrades A. and Fagernas, Zandra and Clayton, Stephan and Garcia, Maxime U. and Neukamm, Judith and Peltzer, Alexander},
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title = {Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager},
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journal = {PeerJ},
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year = {2021},
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volume = {9},
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pages = {e10947},
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doi = {10.7717/peerj.10947},
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pubmed = {33777521},
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section = {articles}
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}
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@article{langer:hal-05224445,
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title = {Empowering bioinformatics communities with Nextflow and nf-core},
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author = {Langer, Björn E and Amaral, Andreia and Baudement, Marie-Odile and Bonath, Franziska and Charles, Mathieu and Chitneedi, Praveen Krishna and Clark, Emily L and Di Tommaso, Paolo and Djebali, Sarah and Ewels, Philip A and Eynard, Sonia and Fellows Yates, James and Fischer, Daniel and Floden, Evan W and Foissac, Sylvain and Gabernet, Gisela and Garcia, Maxime U and Gillard, Gareth and Gundappa, Manu Kumar and Guyomar, Cervin and Hakkaart, Christopher and Hanssen, Friederike and Harrison, Peter W and H{\"o}rtenhuber, Matthias and Kurylo, Cyril and K{\"u}hn, Christa and Lagarrigue, Sandrine and Lallias, Delphine and Macqueen, Daniel J and Miller, Edmund and Mir-Pedrol, J{\'u}lia and Moreira, Gabriel Costa Monteiro and Nahnsen, Sven and Patel, Harshil and Peltzer, Alexander and Pitel, Frederique and Ramayo-Caldas, Yuliaxis and Ribeiro-Dantas, Marcel da C{\^a}mara and Rocha, Dominique and Salavati, Mazdak and Sokolov, Alexey and Espinosa-Carrasco, Jose and Notredame, Cedric and Community, The Nf-Core},
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url = {https://hal.science/hal-05224445},
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journal = {Genome Biology},
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publisher = {BioMed Central},
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volume = {26},
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number = {1},
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pages = {228},
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year = {2025},
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doi = {10.1186/s13059-025-03673-9},
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hal_id = {hal-05224445},
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hal_version = {v1},
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section = {articles}
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}

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