Empowering bioinformatics communities with Nextflow and nf-core.

[en] Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.

Disciplines :

Veterinary medicine & animal health
Computer science

Author, co-author :

Langer, Björn E; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain

Amaral, Andreia; MED. University of Évora, Polo da Mitra, Évora, 7002-554, Portugal ; Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, 1300-477, Portugal

Baudement, Marie-Odile; Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway

Bonath, Franziska; Kungliga Techniska Högskolan, School of Engineering Sciences in Chemistry, Biotechnology and Health at the Department of Gene Technology, Stockholm, Sweden

Charles, Mathieu; INRAE, AgroParisTech, GABI, Université Paris-Saclay, Jouy-en-Josas, F-78350, France ; SIGENAE, INRAE, Jouy-en-Josas, F-78350, France

Chitneedi, Praveen Krishna; Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany

Clark, Emily L; The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin, UK

Di Tommaso, Paolo; Seqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain

Djebali, Sarah; IRSD, Université de Toulouse, INSERM, INRAE, ENVT, Univ Toulouse III - Paul Sabatier (UPS), Toulouse, France

Ewels, Philip A; Seqera, Carrer de Marià Aguiló, 28, Barcelona, 08005, Spain

More authors (34 more)

Language :

English

Title :

Empowering bioinformatics communities with Nextflow and nf-core.

Publication date :

2025

Journal title :

Genome Biology

ISSN :

1474-7596

eISSN :

1474-760X

Publisher :

BioMed Central Ltd, England

Volume :

Issue :

Pages :

228

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://link.springer.com/content/pdf/10.1186/s13059-025-03673-9.pdf

Funders :

EU - European Union
Ministry of Science and Innovation
Generalitat de Catalunya
WSS - Werner Siemens-Stiftung
Carl-Zeiss-Stiftung
DFG - Deutsche Forschungsgemeinschaft

Funding text :

Horizon 2020 research and innovation programme,European Union,815668 (BovReg),815668 (BovReg),817923 (AQUA-FAANG),815668 (BovReg),815668 (BovReg),815668 (BovReg),817998 (GENE-SWitCH),101000236 (GEroNIMO),815668 (BovReg),817998 (GENE-SWitCH),817923 (AQUA-FAANG),817923 (AQUA-FAANG),817998 (GENE-SWitCH),815668 (BovReg),817998 (GENE-SWitCH),815668 (BovReg),817998 (GENE-SWitCH),817923 (AQUA-FAANG),817923 (AQUA-FAANG),815668 (BovReg),101000236 (GEroNIMO),101000213 (HoloRuminant),815668 (BovReg),815668 (BovReg),815668 (BovReg),815668 (BovReg),815668 (BovReg),Spanish Ministry of Science and Innovation,Generalitat de Catalunya,Werner Siemens-Stiftung,Palaeobiotechnology,Horizon Europe programme,European Union,101094718 (EuroFAANG Research Infrastructure),101094718 (EuroFAANG Research Infrastructure),Carl-Zeiss-Stiftung,Certification and Foundations of Safe Machine Learning Systems in Healthcare,Deutsche Forschungsgemeinschaft,EXC 2180\u2014390900677 (iFIT)The EuroFAANG genomics communities have received funding from the European Union\u2019s Horizon 2020 research and innovation programme under Grant Agreement Numbers 817923 (AQUA-FAANG), 815668 (BovReg), 817998 (GENE-SWitCH), 101000226 (RUMIGEN), 101000236 (GEroNIMO), 101000213 (HoloRuminant), and the Horizon Europe programme under Grant Agreement Number 101094718 (EuroFAANG Research Infrastructure). Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them.J.A.F.Y. was supported by Max Planck Society and the Werner Siemens Foundation grant \u201CPalaeobiotechnology\u201D (awarded to Profs. Pierre Stallforth and Christina Warinner).SN acknowledges support by the Carl Zeiss Foundation, project \u201CCertification and Foundations of Safe Machine Learning Systems in Healthcare.\u201D SN is \u201Cgef\u00F6rdert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der L\u00E4nder\u2014EXC 2180\u2014390,900,677 (iFIT).\u201D SN is \u201Cgef\u00F6rdert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der L\u00E4nder\u2014EXC 2124\u2013390,838,134 (CMFI).\u201D This study was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the project NFDI 1/1 \u201CGHGA\u2014German Human Genome-Phenome Archive\u201D (#441,914,366 to SN).CN, BL and JEC have received funding from the Spanish Ministry of Science and Innovation. They acknowledge support from the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI/ https://doi.org/10.13039/501100011033 ), and the Generalitat de Catalunya through the CERCA programme. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under the grant agreement 815,668 (BovReg). They are grateful to the CRG Core Technologies Programme for their support and assistance in this work.

Available on ORBi :

since 12 April 2026

Statistics

Number of views

42 (0 by ULiège)

Number of downloads

22 (0 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenAlex citations

Bibliography

THE Gtex CONSORTIUM The GTEx Consortium atlas of genetic regulatory effects across human tissues Science 369 6509 1318 1330
ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 7414 57 74
H. Kawaji T. Kasukawa A. Forrest P. Carninci Y. Hayashizaki The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types Sci Data 4 1 170113 1:CAS:528:DC%2BC2sXhtl2rur7E
B. Grüning J. Chilton J. Köster R. Dale N. Soranzo M. Van Den Beek et al. Practical computational reproducibility in the life sciences Cell Syst 6 6 631 635
E. Deelman T. Peterka I. Altintas C.D. Carothers K.K. Van Dam K. Moreland et al. The future of scientific workflows Int J High Perform Comput Appl 32 1 159 175
The Galaxy Community The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update Nucleic Acids Res 52 W1 W83 94
Mölder F, Jablonski KP, Letcher B, Hall MB, Tomkins-Tinch CH, Sochat V, et al. Sustainable data analysis with Snakemake [version 2; peer review: 2 approved]. F1000Research. 2021 Apr 19;10(33). Available from: https://f1000research.com/articles/10-33. Cited 2024 Jan 24.
P. Di Tommaso M. Chatzou E.W. Floden P.P. Barja E. Palumbo C. Notredame Nextflow enables reproducible computational workflows Nat Biotechnol 35 4 316 319
L. Wratten A. Wilm J. Göke Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers Nat Methods 18 10 1161 1168 1:CAS:528:DC%2BB3MXitFSmtLrF
About GitHub. GitHub. 2025. Available from: https://github.com/about. Cited 2025 Feb 27.
Gustafsson OJR, Wilkinson SR, Bacall F, Soiland-Reyes S, Leo S, Pireddu L, et al. WorkflowHub: a registry for computational workflows. Sci Data. 2025;12(1):837. https://doi.org/10.1038/s41597-025-04786-3.
L.C. Crosswell J.M. Thornton ELIXIR: a distributed infrastructure for European biological data Trends Biotechnol 30 5 241 242 1:CAS:528:DC%2BC38Xjslelu7o%3D
Galaxy | Tool Shed. Available from: https://toolshed.g2.bx.psu.edu/. Cited 2025 Feb 27.
Snakemake workflow catalog. 2024. Available from: https://snakemake.github.io/snakemake-workflow-catalog/. Cited 2024 Jun 6.
Snakemake-Workflows. 2024. Available from: https://github.com/snakemake-workflows. Cited 2024 Feb 20.
nf-core. 2024. Available from: https://nf-co.re/. Cited 2024 Jun 6.
Grayson S, Marinov D, Katz DS, Milewicz R. Automatic Reproduction of Workflows in the Snakemake Workflow Catalog and nf-core Registries. In: Proceedings of the 2023 ACM Conference on Reproducibility and Replicability. Santa Cruz CA USA: ACM; 2023. p. 74–84. Available from: https://dl.acm.org/doi/10.1145/3589806.3600037. Cited 2023 Jul 5.
P.A. Ewels A. Peltzer S. Fillinger H. Patel J. Alneberg A. Wilm et al. The nf-core framework for community-curated bioinformatics pipelines Nat Biotechnol 38 3 276 278 1:CAS:528:DC%2BB3cXjtFelsbo%3D
D.R. Scott H. Cho C.K. Day A.T. Deller M. Glowacki K. Gourdji et al. CELEBI: the CRAFT effortless localisation and enhanced burst inspection pipeline Astron Comput 1 44 100724
Lehmann F, Frantz D, Becker S, Leser U, Hostert P. FORCE on Nextflow: Scalable Analysis of Earth Observation Data on Commodity Clusters. In: Cong G, Ramanath M, editors. Proceedings of the CIKM 2021 Workshops. Gold Coast, Queensland, Australia: CEUR-WS.org; 2021. (CEUR Workshop Proceedings; vol. 3052). Available from: http://ceur-ws.org/Vol-3052/short12.pdf.
N. Kanakaris N. Karacapilidis Predicting prices of Airbnb listings via graph neural networks and document embeddings: the case of the island of Santorini Procedia Comput Sci 1 219 705 712
Seqeralabs/wave. Seqera; 2024. Available from: https://github.com/seqeralabs/wave. Cited 2024 Feb 20.
Askimed/nf-test. Askimed; 2024. Available from: https://github.com/askimed/nf-test. Cited 2024 Feb 20.
Nextflow-io/nf-validation. nextflow-io; 2024. Available from: https://github.com/nextflow-io/nf-validation. Cited 2024 Feb 20.
Nextflow-io/nf-co2footprint. nextflow-io; 2024. Available from: https://github.com/nextflow-io/nf-co2footprint. Cited 2024 Feb 20.
Nextflow-io/nf-prov. nextflow-io; 2024. Available from: https://github.com/nextflow-io/nf-prov. Cited 2024 Feb 20.
B. Grüning R. Dale A. Sjödin B.A. Chapman J. Rowe C.H. Tomkins-Tinch et al. Bioconda: sustainable and comprehensive software distribution for the life sciences Nat Methods 15 7 475 476
L.F. da Veiga B.A. Grüning S. Alves Aflitos H.L. Röst J. Uszkoreit H. Barsnes et al. BioContainers: an open-source and community-driven framework for software standardization Bioinformatics 33 16 2580 2582
M.D. Wilkinson M. Dumontier I.J.J. Aalbersberg G. Appleton M. Axton A. Baak et al. The FAIR guiding principles for scientific data management and stewardship Sci Data 3 1 160018
M. Barker N.P. Chue Hong D.S. Katz A.L. Lamprecht C. Martinez-Ortiz F. Psomopoulos et al. Introducing the FAIR principles for research software Sci Data 9 1 622
P. Ewels M. Magnusson S. Lundin M. Käller MultiQC: summarize analysis results for multiple tools and samples in a single report Bioinformatics 32 19 3047 3048 1:CAS:528:DC%2BC28XhvFCmtLzN
Harrison PW, Sokolov A, Nayak A, Fan J, Zerbino D, Cochrane G, et al. The FAANG Data Portal: Global, Open-Access, “FAIR”, and richly validated genotype to phenotype data for high-quality functional annotation of animal genomes. Front Genet. 2021; 12. Available from: https://doi.org/10.3389/fgene.2021.639238. Cited 2024 Jan 24.
Release v19 (31/10/2024) - Genomics England Research Environment User Guide. Available from: https://re-docs.genomicsengland.co.uk/release19/. Cited 2025 Feb 27.
Genomics England Case Study. WEKA. 2020. Available from: https://www.weka.io/resources/case-study/genomics-england-case-study/. Cited 2025 Feb 27.
The Darwin Tree of Life Project Consortium Sequence locally, think globally: the Darwin Tree of Life Project Proc Natl Acad Sci 119 4 e2115642118
H.A. Lewin S. Richards E. Lieberman Aiden M.L. Allende J.M. Archibald M. Bálint et al. The Earth BioGenome project 2020: starting the clock Proc Natl Acad Sci 119 4 e2115635118 1:CAS:528:DC%2BB38XksVKjs7o%3D
M. Jain H.E. Olsen B. Paten M. Akeson The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community Genome Biol 17 1 239
L. Andersson A.L. Archibald C.D. Bottema R. Brauning S.C. Burgess D.W. Burt et al. Coordinated international action to accelerate genome-to-phenome with FAANG, the functional annotation of animal genomes project Genome Biol 16 1 57
A European infrastructure for farmed animal genotype to phenotype research. 2022. Available from: https://cordis.europa.eu/project/id/101094718. Cited 2024 Jan 24.
E.L. Clark A.L. Archibald H.D. Daetwyler M.A.M. Groenen P.W. Harrison R.D. Houston et al. From FAANG to fork: application of highly annotated genomes to improve farmed animal production Genome Biol 21 1 285
I.A. Johnston M.P. Kent P. Boudinot M. Looseley L. Bargelloni S. Faggion et al. Advancing fish breeding in aquaculture through genome functional annotation Aquaculture 30 583 740589
S. Liu Y. Gao O. Canela-Xandri S. Wang Y. Yu W. Cai et al. A multi-tissue atlas of regulatory variants in cattle Nat Genet 54 9 1438 1447 1:CAS:528:DC%2BB38XitFWltLvI
J. Teng Y. Gao H. Yin Z. Bai S. Liu H. Zeng et al. A compendium of genetic regulatory effects across pig tissues Nat Genet 56 1 112 123 1:CAS:528:DC%2BB2cXlvFCgtg%3D%3D
Guan D, Bai Z, Zhu X, Zhong C, Hou Y, Zhu D, et al. Genetic regulation of gene expression across multiple tissues in chickens. Nat Genet. 2025;57(5):1298–308. https://doi.org/10.1038/s41588-025-02155-9.
R. Leng G. Viry M. García-Sancho J. Lowe M. Wong N. Vermeulen The sequences and the sequencers: what can a mixed-methods approach reveal about the history of genomics? Hist Stud Nat Sci 52 3 277 319
Watson M, Law A, Archibald A, Kuo R, Harrison P, Martin F, et al. Deliverable D2.1 Reproducible, scale-able workflows for FAANG data analysis; Available from: https://www.gene-switch.eu/uploads/1/2/6/6/126678735/deliverable_d2.1.pdf. Cited 2025 Feb 27.
S. Guizard K. Miedzinska J. Smith J. Smith R.I. Kuo M. Davey et al. nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing Bioinformatics 39 5 btad150 1:CAS:528:DC%2BB3sXhvVSrt7%2FE
C. Kurylo C. Guyomar S. Foissac S. Djebali TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data NAR Genomics Bioinform 5 4 lqad089
Salavati M, Espinosa-Carrasco J. MazdaX/nf-cage: nf-cage. Zenodo; 2022. Available from: https://zenodo.org/records/6855541. Cited 2024 Jan 25.
Nextflow and nf-core. Chan Zuckerberg Initiative. Available from: https://chanzuckerberg.com/eoss/proposals/nextflow-and-nf-core/. Cited 2025 Feb 10.
Nextflow and nf-core: Reproducible Workflows for the Scientific Community - CZI. Chan Zuckerberg Initiative. Available from: https://chanzuckerberg.com/eoss/proposals/nextflow-and-nf-core-reproducible-workflows-for-the-scientific-community/. Cited 2025 Feb 27.
The Galaxy Community The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update Nucleic Acids Res 50 W1 W345 W351
The Galaxy Community. Correction to ‘The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update’. Nucleic Acids Res. 2022;50(15):8999–8999.
V. Jalili E. Afgan Q. Gu D. Clements D. Blankenberg J. Goecks et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update Nucleic Acids Res 48 W1 W395 402 1:CAS:528:DC%2BB3cXis1egu73P
V. Jalili E. Afgan Q. Gu D. Clements D. Blankenberg J. Goecks et al. Corrigendum: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update Nucleic Acids Res 48 14 8205 8207 1:CAS:528:DC%2BB3MXmslaksL8%3D
E. Afgan D. Baker B. Batut M. van den Beek D. Bouvier M. Čech et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Nucleic Acids Res 46 W1 W537 W544 1:CAS:528:DC%2BC1MXosVyrur8%3D
E. Afgan D. Baker M. van den Beek D. Blankenberg D. Bouvier M. Čech et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update Nucleic Acids Res 44 W1 W3 10 1:CAS:528:DC%2BC2sXhtV2itrfM
J. Goecks A. Nekrutenko J. Taylor The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol 11 8 R86
D. Blankenberg G.V. Kuster N. Coraor G. Ananda R. Lazarus M. Mangan et al. Galaxy: a web-based genome analysis tool for experimentalists Curr Protoc Mol Biol 89 1 19.10.1 19.10.21
B. Giardine C. Riemer R.C. Hardison R. Burhans L. Elnitski P. Shah et al. Galaxy: a platform for interactive large-scale genome analysis Genome Res 15 10 1451 1455 1:CAS:528:DC%2BD2MXhtFajurnE
A. Fillbrunn C. Dietz J. Pfeuffer R. Rahn G.A. Landrum M.R. Berthold KNIME for reproducible cross-domain analysis of life science data J Biotechnol 10 261 149 156
M.R. Berthold N. Cebron F. Dill T.R. Gabriel T. Kötter T. Meinl et al. KNIME - the Konstanz information miner: version 2.0 and beyond ACM SIGKDD Explor Newsl 11 1 26 31
Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, et al. Data analysis, machine learning and applications. In 2008. p. 319–26.
J. Köster S. Rahmann Snakemake—a scalable bioinformatics workflow engine Bioinformatics 34 20 3600 3600
J. Köster S. Rahmann Snakemake—a scalable bioinformatics workflow engine Bioinformatics 28 19 2520 2522
S.P. Sadedin B. Pope A. Oshlack Bpipe: a tool for running and managing bioinformatics pipelines Bioinformatics 28 11 1525 1526 1:CAS:528:DC%2BC38Xns1Slt7Y%3D
J.A. Novella P. Emami Khoonsari S. Herman D. Whitenack M. Capuccini J. Burman et al. Container-based bioinformatics with Pachyderm Bioinformatics 35 5 839 846 1:CAS:528:DC%2BC1MXhvV2rsL3I
S. Lampa M. Dahlö J. Alvarsson O. Spjuth SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines GigaScience 8 5 giz044
Voss K, Auwera GV der, Gentry J. Full-stack genomics pipelining with GATK4 + WDL + Cromwell. F1000Research. 2017 8;6(1381). Available from: https://f1000research.com/slides/6-1381. Cited 2024 Jan 26.
J. Vivian A.A. Rao F.A. Nothaft C. Ketchum J. Armstrong A. Novak et al. Toil enables reproducible, open source, big biomedical data analyses Nat Biotechnol 35 4 314 316 1:CAS:528:DC%2BC2sXmtFGhurk%3D
Amstutz P, Crusoe MR, Tijanić N, Chapman B, Chilton J, Heuer M, et al. Common Workflow Language, v1.0. figshare; 2016. Available from: https://figshare.com/articles/dataset/Common_Workflow_Language_draft_3/3115156/2. Cited 2024 Jan 25.