Empowering bioinformatics communities with Nextflow and nf-core

Langer, Björn E.; Amaral, Andreia; Baudement, Marie-Odile; Bonath, Franziska; Charles, Mathieu; Krishna Chitneedi, Praveen; Clark, Emily L.; Di Tommaso, Paolo; Djebali, Sarah; Ramayo-Caldas, Yuliaxis

dc.contributor.author	Langer, Björn E.
dc.contributor.author	Amaral, Andreia
dc.contributor.author	Baudement, Marie-Odile
dc.contributor.author	Bonath, Franziska
dc.contributor.author	Charles, Mathieu
dc.contributor.author	Krishna Chitneedi, Praveen
dc.contributor.author	Clark, Emily L.
dc.contributor.author	Di Tommaso, Paolo
dc.contributor.author	Djebali, Sarah
dc.contributor.author	Ramayo-Caldas, Yuliaxis
dc.contributor.other	Producció Animal	ca
dc.date.accessioned	2025-10-17T09:42:02Z
dc.date.available	2025-10-17T09:42:02Z
dc.date.issued	2025-07-29
dc.identifier.issn	1474-760X	ca
dc.identifier.uri	http://hdl.handle.net/20.500.12327/4783
dc.description.abstract	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.	ca
dc.description.sponsorship	The EuroFAANG genomics communities have received funding from the European Union’s 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. 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—390900677 (iFIT) 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’s 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. SN acknowledges support by the Carl Zeiss Foundation, project “Certification and Foundations of Safe Machine Learning Systems in Healthcare.” SN is “gefördert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Länder—EXC 2180—390,900,677 (iFIT).” SN is “gefördert durch die Deutsche Forschungsgemeinschaft (DFG) im Rahmen der Exzellenzstrategie des Bundes und der Länder—EXC 2124–390,838,134 (CMFI).” This study was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via the project NFDI 1/1 “GHGA—German Human Genome-Phenome Archive” (#441,914,366 to SN). J.A.F.Y. was supported by Max Planck Society and the Werner Siemens Foundation grant “Palaeobiotechnology” (awarded to Profs. Pierre Stallforth and Christina Warinner).
dc.format.extent	15	ca
dc.language.iso	eng	ca
dc.publisher	BioMed Central	ca
dc.relation.ispartof	Genome Biology	ca
dc.rights	Attribution-NonCommercial-NoDerivatives 4.0 International	*
dc.rights.uri	http://creativecommons.org/licenses/by-nc-nd/4.0/	*
dc.title	Empowering bioinformatics communities with Nextflow and nf-core	ca
dc.type	info:eu-repo/semantics/article	ca
dc.description.version	info:eu-repo/semantics/publishedVersion	ca
dc.rights.accessLevel	info:eu-repo/semantics/openAccess
dc.embargo.terms	cap	ca
dc.relation.projectID	EC/H2020/817923/EU/Advancing European Aquaculture by Genome Functional Annotation/AQUA-FAANG	ca
dc.relation.projectID	EC/H2020/815668/EU/Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle/BovReg	ca
dc.relation.projectID	EC/H2020/817998/EU/The regulatory GENomE of SWine and CHicken: functional annotation during development/GENE-SWitCH	ca
dc.relation.projectID	EC/H2020/101000226/EU/Towards improvement of ruminant breeding through genomic and epigenomic approaches/RUMIGEN	ca
dc.relation.projectID	EC/H2020/101000236/EU/Genome and Epigenome eNabled breedIng in MOnogastrics/GEroNIMO	ca
dc.relation.projectID	EC/H2020/101000213/EU/Understanding microbiomes of the ruminant holobiont/HoloRuminant	ca
dc.relation.projectID	EC/H2020/101094718/EU/A European infrastructure for farmed animal genotype to phenotype research/EuroFAANG	ca
dc.relation.projectID	MICINN/Programa Estatal de generación del conocimiento y fortalecimiento científico y tecnológico del sistema I+D+I/CEX2020-001049-S/ES/	ca
dc.subject.udc	57	ca
dc.identifier.doi	https://doi.org/10.1186/s13059-025-03673-9	ca
dc.contributor.group	Genètica i Millora Animal	ca