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The nf-core project

Latest preprint, with updates to Nextflow and nf-core and a case study about adoption by EuroFAANG:

Empowering bioinformatics communities with Nextflow and nf-core

Bjorn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen, Peter W. Harrison, Matthias Hortenhuber, Cyril Kurylo, Christa Kuhn, Sandrine Lagarrigue, Delphine Lallias, Daniel J. Macqueen, Edmund Miller, Julia Mir-Pedrol, Gabriel Costa Monteiro Moreira, Sven Nahnsen, Harshil Patel, Alexander Peltzer, Frederique Pitel, Yuliaxis Ramayo-Caldas, Marcel da Camara Ribeiro-Dantas, Dominique Rocha, Mazdak Salavati, Alexey Sokolov, Jose Espinosa-Carrasco, Cedric Notredame, nf-core community

bioRxiv 2024.05.10.592912; doi: 10.1101/2024.05.10.592912

Main publication for the main nf-core paper, describing the community and framework:

The nf-core framework for community-curated bioinformatics pipelines

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen

Nat Biotechnology (2020); doi: 10.1038/s41587-020-0439-x

ReadCube: View full text

Preprint for the main nf-core paper (significantly different from the final Nature Biotech paper):

nf-core: Community curated bioinformatics pipelines

Philip Ewels, Alexander Peltzer, Sven Fillinger, Johannes Alneberg, Harshil Patel, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen

bioRxiv 610741; doi: 10.1101/610741

Article in Nature describing scientific workflows (including nf-core):

Workflow systems turn raw data into scientific knowledge

Nextflow

Main publication for Nextflow:

Nextflow enables reproducible computational workflows

Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo & Cedric Notredame

Nat Biotechnology (2017); doi: 10.1038/nbt.3820

Pipeline publications

nf-core/airrflow

nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework

Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Yann Lee, Cole Jensen, David Ladd, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C Kowarik, Sven Nahnsen, Steven H Kleinstein

bioRxiv 2024.01.18.576147 doi: 10.1101/2024.01.18.576147

nf-core/ampliseq

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen and Sara Kleindienst

Frontiers in Microbiology (2020) doi: 10.3389/fmicb.2020.550420

nf-core/callingcards

Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues

Yen, A., Mateusiak, C., Sarafinovska, S., Gachechiladze, M. A., Guo, J., Chen, X., Moudgil, A., Cammack, A. J., Hoisington-Lopez, J., Crosby, M., Brent, M. R., Mitra, R. D., Dougherty, J. D.

Current protocols vol. 3,9 (2023) doi: 10.1002/cpz1.883

nf-core/circrna

nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs.

Barry Digby, Stephen P. Finn, & Pilib Ó Broin

BMC Bioinformatics 24, 27 (2023) doi: 10.1186/s12859-022-05125-8

nf-core/coproid

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Maxime Borry, Bryan Cordova, Angela Perri, Marsha Wibowo, Tanvi Prasad Honap, Jada Ko, Jie Yu, Kate Britton, Linus Girdland-Flink, Robert C. Power, Ingelise Stuijts, Domingo C. Salazar-Garcia, Courtney Hofman, Richard Hagan, Thérèse Samdapawindé Kagoné, Nicolas Meda, Hélène Carabin, David Jacobson, Karl Reinhard, Cecil Lewis, Aleksandar Kostic, Choongwon Jeong, Alexander Herbig, Alexander Hübner, Christina Warinner

PeerJ, 9001 (2020); doi: 10.7717/peerj.9001

nf-core/diaproteomics

DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics

Leon Bichmann, Shubham Gupta, George Rosenberger, Leon Kuchenbecker, Timo Sachsenberg, Phil Ewels, Oliver Alka, Julianus Pfeuffer, Oliver Kohlbacher, and Hannes Röst

J. Proteome Res. (2021) doi: 10.1021/acs.jproteome.1c00123

nf-core/eager

Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer

PeerJ, 9

(2021); doi: 10.7717/peerj.10947

nf-core/hgtseq

hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer

Simone Carpanzano, Mariangela Santorsola, nf-core community and Francesco Lescai

Int. J. Mol. Sci. 2022, 23(23), 14512 doi: 10.3390/ijms232314512

nf-core/hicar

HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.

Xiaolin Wei, Yu Xiang, Derek T. Peters, Choiselle Marius, Tongyu Sun, Ruocheng Shan, Jianhong Ou, Xin Lin, Feng Yue, Wei Li, Kevin W. Southerland, Yarui Diao

Molecular Cell (2022); doi: 10.1016/j.molcel.2022.01.023

nf-core/isoseq

nf-core/isoseq: Simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

Sébastien Guizard, Katarzyna Miedzinska, Jacqueline Smith, Jonathan Smith, Richard Kuo, Megan Davey, Alan Archibald, Michael Bryan Watson Bioinformatics 2023 Mar; doi: 10.1093/bioinformatics/btad150

nf-core/imcyto

Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry.

Febe van Maldegem, Karishma Valand, Megan Cole, Harshil Patel, Mihaela Angelova, Sareena Rana, Emma Colliver, Katey Enfield, Nourdine Bah, Gavin Kelly, Victoria Siu Kwan Tsang, Edurne Mugarza, Christopher Moore, Philip Hobson, Dina Levi, Miriam Molina, Charles Swanton & Julian Downward

Nat Commun. 2021 Oct 8;12(1):5906; doi: 10.1038/s41467-021-26214-x

nf-core/lncpipe

LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data.

Qi Zhao, Yu Sun, Dawei Wang, Hongwan Zhang, Kai Yu, Jian Zheng, Zhixiang Zuo.

Journal of Genetics and Genomics 20;45(7):399-401 (2018) doi: 10.1016/j.jgg.2018.06.005

nf-core/mag

nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning

Sabrina Krakau, Daniel Straub, Hadrien Gourlé, Gisela Gabernet, Sven Nahnsen

NAR Genomics and Bioinformatics, Vol 4, Issue 1 (2022); doi: 10.1093/nargab/lqac007

nf-core/marsseq

nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments

Martin Proks, Jose Alejandro Romero Herrera, Jakub Sedzinski, Joshua M Brickman bioRxiv 2023.06.28.546862; doi: 10.1101/2023.06.28.546862

nf-core/mhcquant

MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics

Leon Bichmann, Annika Nelde, Michael Ghosh, Lukas Heumos, Christopher Mohr, Alexander Peltzer, Leon Kuchenbecker, Timo Sachsenberg, Juliane S. Walz, Stefan Stevanović, Hans-Georg Rammensee, and Oliver Kohlbacher

Journal of Proteome Research 18(11), 3876-3884 (2019) doi: 10.1021/acs.jproteome.9b00313

MHCquant2 refines immunopeptidomics tumor antigen discovery

Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann, Lennart Martens, Marissa L. Dubbelaar, Sven Nahnsen, Juliane S. Walz

ResearchSquare 2024.12.04 doi: 10.21203/rs.3.rs-5560023/v1

nf-core/nanostring

An analysis pipeline for Nanostring nCounter expression data.

Alexander Peltzer, Christopher Mohr, Kai B. Stadermann, Matthias Zwick, Ramona Schmid.

Oxford Bioinformatics; doi: 10.1093/bioinformatics/btae019/7517109

nf-core/nanoseq

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

Ying Chen, Nadia M. Davidson, Yuk Kei Wan, Harshil Patel, Fei Yao, Hwee Meng Low, Christopher Hendra, Laura Watten, Andre Sim, Chelsea Sawyer, Viktoriia Iakovleva, Puay Leng Lee, Lixia Xin, Hui En Vanessa Ng, Jia Min Loo, Xuewen Ong, Hui Qi Amanda Ng, Jiaxu Wang, Wei Qian Casslynn Koh, Suk Yeah Polly Poon, Dominik Stanojevic, Hoang-Dai Tran, Kok Hao Edwin Lim, Shen Yon Toh, Philip Andrew Ewels, Huck-Hui Ng, N.Gopalakrishna Iyer, Alexandre Thiery, Wee Joo Chng, Leilei Chen, Ramanuj DasGupta, Mile Sikic, Yun-Shen Chan, Boon Ooi Patrick Tan, Yue Wan, Wai Leong Tam, Qiang Yu, Chiea Chuan Khor, Torsten Wüstefeld, Ploy N. Pratanwanich, Michael I. Love, Wee Siong Sho Goh, Sarah B. Ng, Alicia Oshlack, Jonathan Göke, SG-NEx consortium

bioRxiv 610741; doi: 10.1101/610741

nf-core/omicsgenetraitassociation

A methodology for gene level omics-WAS integration identifies genes influencing traits associated with cardiovascular risks: the Long Life Family Study

Sandeep Acharya, Shu Liao, Wooseok J. Jung, Yu S. Kang, Vaha Akbary Moghaddam, Mary F. Feitosa, Mary K. Wojczynski, Shiow Lin, Jason A. Anema, Karen Schwander, Jeff O. Connell, Michael A. Province & Michael R. Brent.

Hum. Genet. (2024) doi: 10.1007/s00439-024-02701-1

nf-core/pangenome

Cluster-efficient pangenome graph construction with nf-core/pangenome

Simon Heumos, Michael L Heuer, Friederike Hanssen, Lukas Heumos, Andrea Guarracino, Peter Heringer, Philipp Ehmele, Pjotr Prins, Erik Garrison, Sven Nahnsen.

Bioinformatics (2024) doi: 10.1093/bioinformatics/btae609

nf-core/sarek

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 2; peer review: 2 approved]

Maxime Garcia, Szilveszter Juhos, Malin Larsson, Pall I. Olason, Marcel Martin, Jesper Eisfeldt, Sebastian DiLorenzo, Johanna Sandgren, Teresita Díaz De Ståhl, Philip Ewels, Valtteri Wirta, Monica Nistér, Max Käller, Björn Nystedt

F1000Research, 9:63 (2020) doi: 10.12688/f1000research.16665.2

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery

Friederike Hanssen, Maxime U. Garcia, Lasse Folkersen, Anders Sune Pedersen, Francesco Lescai, Susanne Jodoin, Edmund Miller, Matthias Seybold, Oskar Wacker, Nicholas Smith, Gisela Gabernet, Sven Nahnsen

NAR Genomics and Bioinformatics, 6(2)

(2024) doi: 10.1093/nargab/lqae031

nf-core/scflow

scFlow: A Scalable and Reproducible Analysis Pipeline for Single-Cell RNA Sequencing Data

Combiz Khozoie, Nurun Fancy, Mahdi M. Marjaneh, Alan E. Murphy, Paul M. Matthews, Nathan Skene

bioRxiv 2021.08.16.456499 doi: 10.1101/2021.08.16.456499

nf-core/taxprofiler

nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling

Sofia Stamouli, Moritz E. Beber, Tanja Normark, Thomas A Christensen II, Lili Andersson-Li, Maxime Borry, Mahwash Jamy, nf-core community, James A. Fellows Yates

bioRxiv (2023) doi: 10.1101/2023.10.20.563221
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