Empowering bioinformatics communities with Nextflow and nf-core
Empowering bioinformatics communities with Nextflow and nf-core
Abstract Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line solutions such as Nextflow and Snakemake. We report on recent developments in the nf-core and Nextflow frameworks that have led to widespread adoption across many scientific communities. We describe how adopting nf-core standards enables faster development, improved interoperability, and collaboration with the >8,000 members of the nf-core community. The recent development of Nextflow Domain-Specific Language 2 (DSL2) allows pipeline components to be shared and combined across projects. The nf-core community has harnessed this with a library of modules and subworkflows that can be integrated into any Nextflow pipeline, enabling research communities to progressively transition to nf-core best practices. We present a case study of nf-core adoption by six European research consortia, grouped under the EuroFAANG umbrella and dedicated to farmed animal genomics. We believe that the process outlined in this report can inspire many large consortia to seek harmonisation of their data analysis procedures.
Notredame Cedric、Charles Mathieu、Pitel Frederique、Amaral Andreia、Bonath Franziska、Chitneedi Praveen Krishna、Clark Emily L.、Djebali Sarah、Yates James A. Fellows、Foissac Sylvain、Gillard Gareth、Gundappa Manu Kumar、Hakkaart Christopher、Harrison Peter W.、Kurylo Cyril、Macqueen Daniel J.、Langer Bj?rn E.、Rocha Dominique、Salavati Mazdak、Sokolov Alexey、Mir-Pedrol J¨2lia、Peltzer Alexander、Floden Evan W.、Lallias Delphine、Patel Harshil、Espinosa-Carrasco Jose、the nf-core community.、Di Tommaso Paolo、Lagarrigue Sandrine、Baudement Marie-Odile、Guyomar Cervin、Hanssen Friederike、Eynard Sonia、H?rtenhuber Matthias、Ewels Philip A.、Garcia Maxime U.、Gabernet Gisela、Fischer Daniel、Ramayo-Caldas Yuliaxis、Moreira Gabriel Costa Monteiro、Miller Edmund、K¨1hn Christa、da Camara Ribeiro-Dantas Marcel、Nahnsen Sven
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology||Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF)INRAE, AgroParisTech, GABI, Universit¨| Paris-Saclay||SIGENAE, INRAEGenPhySE, Universit¨| de Toulouse, INRAE, ENVTMED. University of ¨|vora||Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of LisbonKungliga Techniska H?gskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene TechnologyResearch Institute for Farm Animal Biology (FBN)The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghIRSD, Universit¨| de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS)Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology||Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Kn?ll Institute||Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Kn?ll InstituteGenPhySE, Universit¨| de Toulouse, INRAE, ENVTCentre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life SciencesThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghSeqera, Carrer de Mari¨¤ Aguil¨?European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusGenPhySE, Universit¨| de Toulouse, INRAE, ENVTThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyINRAE, AgroParisTech, GABI, Universit¨| Paris-SaclayThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh||Dairy Research Innovation Centre, South and West Faculty, Scotland?ˉs Rural CollegeEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome CampusQuantitative Biology Center (QBiC), University of T¨1bingenBoehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Stra?e 65Seqera, Carrer de Mari¨¤ Aguil¨?INRAE, AgroParisTech, GABI, Universit¨| Paris-SaclaySeqera, Carrer de Mari¨¤ Aguil¨?Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologySeqera, Carrer de Mari¨¤ Aguil¨?PEGASE, INRAE, Institut AgroCentre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life SciencesGenPhySE, Universit¨| de Toulouse, INRAE, ENVTBiomedical Data Science, Department of Computer Science, University of T¨1bingen||Quantitative Biology Center (QBiC), University of T¨1bingen||M3 Research Center, Faculty of Medicine, University of T¨1bingenGenPhySE, Universit¨| de Toulouse, INRAE, ENVTDepartment of Immunology, Genetics and Pathology, Uppsala University||SciLifeLab, Uppsala UniversitySeqera, Carrer de Mari¨¤ Aguil¨?Seqera, Carrer de Mari¨¤ Aguil¨?Department of Pathology, Yale School of Medicine. New HavenNatural Resources Institute Finland (Luke), Applied Statistical MethodsAnimal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA)Unit of Animal Genomics, GIGA & Faculty of Veterinary Medicine, University of Li¨¨geDepartment of Biological Sciences and Center for Systems Biology, The University of Texas at DallasResearch Institute for Farm Animal Biology (FBN)||Friedrich-Loeffler-Institut (FLI)Seqera, Carrer de Mari¨¤ Aguil¨?||Postgraduate Program in Biotechnology at Universidade Potiguar (UnP) ¨C Natal/RNBiomedical Data Science, Department of Computer Science, University of T¨1bingen||Quantitative Biology Center (QBiC), University of T¨1bingen||M3 Research Center, Faculty of Medicine, University of T¨1bingen||Institute for Bioinformatics and Medical Informatics (IBMI), University of T¨1bingen
生物科学研究方法、生物科学研究技术生物科学现状、生物科学发展信息科学、信息技术
Notredame Cedric,Charles Mathieu,Pitel Frederique,Amaral Andreia,Bonath Franziska,Chitneedi Praveen Krishna,Clark Emily L.,Djebali Sarah,Yates James A. Fellows,Foissac Sylvain,Gillard Gareth,Gundappa Manu Kumar,Hakkaart Christopher,Harrison Peter W.,Kurylo Cyril,Macqueen Daniel J.,Langer Bj?rn E.,Rocha Dominique,Salavati Mazdak,Sokolov Alexey,Mir-Pedrol J¨2lia,Peltzer Alexander,Floden Evan W.,Lallias Delphine,Patel Harshil,Espinosa-Carrasco Jose,the nf-core community.,Di Tommaso Paolo,Lagarrigue Sandrine,Baudement Marie-Odile,Guyomar Cervin,Hanssen Friederike,Eynard Sonia,H?rtenhuber Matthias,Ewels Philip A.,Garcia Maxime U.,Gabernet Gisela,Fischer Daniel,Ramayo-Caldas Yuliaxis,Moreira Gabriel Costa Monteiro,Miller Edmund,K¨1hn Christa,da Camara Ribeiro-Dantas Marcel,Nahnsen Sven.Empowering bioinformatics communities with Nextflow and nf-core[EB/OL].(2025-03-28)[2025-07-16].https://www.biorxiv.org/content/10.1101/2024.05.10.592912.点此复制
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