{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T06:10:11Z","timestamp":1756447811926,"version":"3.44.0"},"reference-count":50,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T00:00:00Z","timestamp":1756425600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>The increasing adoption of high-throughput \u201comics\u201d technologies has heightened the demand for standardized, scalable, and reproducible bioinformatics workflows. Nextflow and nf-core provide a robust framework for researchers, particularly early- and mid-career researchers (EMCRs), to navigate complex data analysis. At The Kids Research Institute Australia, we implemented a structured approach to bioinformatics capacity building using these tools. This perspective presents nine practical rules derived from lessons learnt, which facilitated the successful adoption of Nextflow and nf-core, addressing implementation challenges, knowledge gaps, resource allocation, and community support. Our experience serves as a guide for institutions aiming to establish sustainable bioinformatics capabilities and empower EMCRs.<\/jats:p>","DOI":"10.3389\/fbinf.2025.1610015","type":"journal-article","created":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T05:43:47Z","timestamp":1756446227000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers\u2013focused program at The Kids Research Institute Australia"],"prefix":"10.3389","volume":"5","author":[{"given":"Patricia","family":"Agudelo-Romero","sequence":"first","affiliation":[]},{"given":"Talya","family":"Conradie","sequence":"additional","affiliation":[]},{"given":"Jose Antonio","family":"Caparros-Martin","sequence":"additional","affiliation":[]},{"given":"David Jimmy","family":"Martino","sequence":"additional","affiliation":[]},{"given":"Anthony","family":"Kicic","sequence":"additional","affiliation":[]},{"given":"Stephen Michael","family":"Stick","sequence":"additional","affiliation":[]},{"given":"Christopher","family":"Hakkaart","sequence":"additional","affiliation":[]},{"given":"Abhinav","family":"Sharma","sequence":"additional","affiliation":[]},{"name":"the Theme Collaboration Group","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,8,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"W83","DOI":"10.1093\/NAR\/GKAE410","article-title":"The galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"Abueg","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B2","unstructured":"Nextflow-BioWiki\n          \n          \n            \n              Agudelo-Romero\n              P.\n            \n            \n              Conradie\n              T.\n            \n            \n              Caparros-Martin\n              J.\n            \n            \n              Stick\n              S.\n            \n            \n              Christopher\n              H.\n            \n            \n              Sharma\n              A.\n            \n          \n          \n          2023"},{"key":"B3","doi-asserted-by":"publisher","first-page":"AB243","DOI":"10.1016\/j.jaci.2023.11.779","article-title":"Nasal and amnion methylomes: biomarkers for smoke exposure and maternal asthma","volume":"153","author":"Agudelo-Romero","year":"2024","journal-title":"J. Allergy Clin. Immunol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14963685","article-title":"A Nextflow-Based automated pipeline for viral assembly and characterisation (EVEREST)","author":"Agudelo-Romero","year":"2025"},{"key":"B5","volume-title":"The java programming language","author":"Arnold","year":"2005"},{"key":"B6","doi-asserted-by":"publisher","first-page":"e1009592","DOI":"10.1371\/journal.pcbi.1009592","article-title":"Ten simple rules for developing bioinformatics capacity at an academic institution","volume":"17","author":"Aron","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"2000134","DOI":"10.1002\/bies.202000134","article-title":"Enhancing bioinformatics and genomics courses: building capacity and skills via lab meeting activities","volume":"42","author":"Boudabous","year":"2020","journal-title":"BioEssays"},{"key":"B8","doi-asserted-by":"publisher","first-page":"e1009823","DOI":"10.1371\/journal.pcbi.1009823","article-title":"Ten simple rules for making a software tool workflow-ready","volume":"18","author":"Brack","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"e1008645","DOI":"10.1371\/journal.pcbi.1008645","article-title":"Ten simple rules for getting started with command-line bioinformatics","volume":"17","author":"Brandies","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e1005871","DOI":"10.1371\/journal.pcbi.1005871","article-title":"Ten simple rules for biologists learning to program","volume":"14","author":"Carey","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"2580","DOI":"10.1093\/bioinformatics\/btx192","article-title":"BioContainers: an open-source and community-driven framework for software standardization","volume":"33","author":"da Veiga Leprevost","year":"2017","journal-title":"Bioinformatics"},{"key":"B12","doi-asserted-by":"publisher","first-page":"911861","DOI":"10.3389\/fmed.2022.911861","article-title":"Advances and trends in omics technology development","volume":"9","author":"Dai","year":"2022","journal-title":"Front. Med. (Lausanne)"},{"key":"B13","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/S41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Dale","year":"2018","journal-title":"Nat. Methods"},{"key":"B14","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/NBT.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"DI Tommaso","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14502249","article-title":"nf-core\/methylseq: endless tofu","author":"Ewels","year":"2024"},{"key":"B17","doi-asserted-by":"publisher","first-page":"e1006671","DOI":"10.1371\/JOURNAL.PCBI.1006671","article-title":"Ten simple rules for organizing a webinar series","volume":"15","author":"Fadlelmola","year":"2019","journal-title":"PLoS Comput. Biol."},{"key":"B18","volume-title":"Enabling national step changes in bioinformatics through ABLeS, the Australian BioCommons leadership share","author":"Gustafsson","year":"2023"},{"key":"B19","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1038\/s41597-025-04786-3","article-title":"WorkflowHub: a registry for computational workflows","volume":"12","author":"Gustafsson","year":"2025","journal-title":"Sci. Data"},{"key":"B20","doi-asserted-by":"publisher","first-page":"e1008119","DOI":"10.1371\/journal.pcbi.1008119","article-title":"Ten simple rules to increase computational skills among biologists with code clubs","volume":"16","author":"Hagan","year":"2020","journal-title":"PLoS Comput. Biol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"00618","DOI":"10.1183\/23120541.00618-2025","article-title":"Conservation of gene expression patterns between the amniotic and nasal epithelium at birth","author":"Hancock","year":"2025","journal-title":"ERJ Open Res."},{"key":"B22","doi-asserted-by":"publisher","first-page":"e1010750","DOI":"10.1371\/journal.pcbi.1010750","article-title":"Ten simple rules for implementing open and reproducible research practices after attending a training course","volume":"19","author":"Heise","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"1070390","DOI":"10.3389\/frma.2023.1070390","article-title":"Building awareness and capacity of bioinformatics and open science skills in Kenya: a sensitize, train, hack, and collaborate model","volume":"8","author":"Karega","year":"2023","journal-title":"Front. Res. Metr. Anal."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/biomedinformatics3010001","article-title":"Trecode: a FAIR eco-system for the analysis and archiving of omics data in a combined diagnostic and research setting","volume":"3","author":"Kerstens","year":"2023","journal-title":"BioMedInformatics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1210\/me.2014-1036","article-title":"Editorial: do you see what I see? quality, reliability, and reproducibility in biomedical research","volume":"28","author":"Kraus","year":"2014","journal-title":"Mol. Endocrinol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"e0177459","DOI":"10.1371\/journal.pone.0177459","article-title":"Singularity: scientific containers for mobility of compute","volume":"12","author":"Kurtzer","year":"2017","journal-title":"PLoS One"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1101\/2024.05.10.592912","article-title":"Empowering bioinformatics communities with nextflow and nf-core","author":"Langer","year":"2024"},{"key":"B28","doi-asserted-by":"publisher","first-page":"e1006923","DOI":"10.1371\/journal.pcbi.1006923","article-title":"From trainees to trainers to instructors: sustainably building a national capacity in bioinformatics training","volume":"15","author":"McGrath","year":"2019","journal-title":"PLoS Comput. Biol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"rcmb.2025-0046MA","DOI":"10.1165\/RCMB.2025-0046MA","article-title":"Optimisation of DNA extraction from nasal lining fluid to assess the nasal microbiome using third-generation sequencing","author":"Montgomery","year":"2025","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.8222875","article-title":"nf-core\/atacseq","author":"Patel","year":"2023"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.13691888","article-title":"nf-core\/rnaseq: nf-core\/rnaseq v3","volume":"15","author":"Patel","year":"2024"},{"key":"B32","doi-asserted-by":"publisher","article-title":"Acacia object storage","year":"","DOI":"10.48569\/nfe9-a426"},{"key":"B33","doi-asserted-by":"publisher","article-title":"Garrawarla GPU cluster","year":"","DOI":"10.48569\/gskb-tp15"},{"key":"B34","doi-asserted-by":"publisher","article-title":"Nimbus research cloud","year":"","DOI":"10.48569\/v0j3-qd51"},{"key":"B35","doi-asserted-by":"publisher","article-title":"Setonix supercomputer","year":"","DOI":"10.48569\/18sb-8s43"},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14360028","article-title":"nf-core\/scrnaseq: 3.0.0","author":"Peltzer","year":""},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.13928318","article-title":"nf-core\/smrnaseq: V2.4.0 - 2024-10-14 - gray zinc dalmation patch","author":"Peltzer","year":""},{"key":"B38","doi-asserted-by":"publisher","first-page":"107739","DOI":"10.1016\/j.biotechadv.2021.107739","article-title":"Using machine learning approaches for multi-omics data analysis: a review","volume":"49","author":"Reel","year":"2021","journal-title":"Biotechnol. Adv."},{"key":"B39","doi-asserted-by":"publisher","first-page":"e1010705","DOI":"10.1371\/journal.pcbi.1010705","article-title":"Ten simple rules and a template for creating workflows-as-applications","volume":"18","author":"Roach","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.17504\/protocols.io.36wgq6rdolk5\/v2","article-title":"Metagenome processing in clinical setting for respiratory pathogens v2","author":"Sharma","year":""},{"key":"B41","doi-asserted-by":"publisher","first-page":"7608","DOI":"10.21105\/JOSS.07608","article-title":"target-methylseq-qc: a lightweight pipeline for collecting metrics from targeted sequence mapping files","volume":"10","author":"Sharma","year":"","journal-title":"J. Open Source Softw."},{"key":"B42","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big data: astronomical or genomical?","volume":"13","author":"Stephens","year":"2015","journal-title":"PLoS Biol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s13104-022-05949-w","article-title":"Reforms to improve reproducibility and quality must be coordinated across the research ecosystem: the view from the UKRN local network leads","volume":"15","author":"Stewart","year":"2022","journal-title":"BMC Res. Notes"},{"key":"B44","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14167648","article-title":"nf-core\/ampliseq: Ampliseq version 2.12.0","author":"Straub","year":"2024"},{"key":"B45","doi-asserted-by":"publisher","first-page":"lqae040","DOI":"10.1093\/nargab\/lqae040","article-title":"Nextflow vs. plain bash: different approaches to the parallelization of SNP calling from the whole genome sequence data","volume":"6","author":"Sztuka","year":"2024","journal-title":"Nar. Genom Bioinform"},{"key":"B46","doi-asserted-by":"publisher","first-page":"854752","DOI":"10.3389\/fgene.2022.854752","article-title":"Unsupervised multi-omics data integration methods: a comprehensive review","volume":"13","author":"Vahabi","year":"2022","journal-title":"Front. Genet."},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.10209675","article-title":"nf-core\/differentialabundance: V1.4.0 - 2023-11-27","author":"Wacker","year":"2023"},{"key":"B48","doi-asserted-by":"publisher","first-page":"e1009440","DOI":"10.1371\/journal.pcbi.1009440","article-title":"Ten simple rules for training yourself in an emerging field","volume":"17","author":"Woelmer","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"B49","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.14526076","article-title":"nf-core\/mag: mag 3.3.0 - red reindeer","author":"Yates","year":"2024"},{"key":"B50","doi-asserted-by":"publisher","first-page":"e1005399","DOI":"10.1371\/journal.pcbi.1005399","article-title":"Ten simple rules for responsible big data research","volume":"13","author":"Zook","year":"2017","journal-title":"PLoS Comput. Biol."}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2025.1610015\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T05:43:50Z","timestamp":1756446230000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2025.1610015\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,29]]},"references-count":50,"alternative-id":["10.3389\/fbinf.2025.1610015"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2025.1610015","relation":{},"ISSN":["2673-7647"],"issn-type":[{"value":"2673-7647","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,8,29]]},"article-number":"1610015"}}