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{{Short description|Open-Source Workflow Management Platform}}{{Multiple issues|{{primary sources|date=October 2022}}{{advert|date=September 2022}}}}

factoids

}}Nextflow is a scientific workflow system predominantly used for bioinformatic data analyses. It imposes standards on how to programmatically author a sequence of dependent compute steps and enables their execution on various local and cloud resources.BOOK, 10.1007/978-1-4939-9074-0_24, 7613310, 31278683, Scalable Workflows and Reproducible Data Analysis for Genomics, Evolutionary Genomics, Methods in Molecular Biology, 2019, Strozzi, Francesco, Janssen, Roel, Wurmus, Ricardo, Crusoe, Michael R., Githinji, George, Di Tommaso, Paolo, Belhachemi, Dominique, Möller, Steffen, Smant, Geert, De Ligt, Joep, Prins, Pjotr, 1910, 723–745, 978-1-4939-9073-3, JOURNAL, 10.1093/bib/bbaa116, 34020539, Comparison of high-throughput single-cell RNA sequencing data processing pipelines, 2021, Gao, Mingxuan, Ling, Mingyi, Tang, Xinwei, Wang, Shun, Xiao, Xu, Qiao, Ying, Yang, Wenxian, Yu, Rongshan, Briefings in Bioinformatics, 22, 3, Nextflow was conceived at the Centre for Genomic Regulation in Barcelona, Spain, but has since found world-wide adoption in biomedical and genomics research facilities and laboratories.

Purpose

Many scientific data analyses require a significant amount of sequential processing steps. Custom scripts may suffice when developing new methods or infrequently running a particular analysis, but scale poorly to complex task successions or many samples.JOURNAL, Wratten, Laura, Wilm, Andreas, Göke, Jonathan, Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers, Nature Methods, 18, 10, 1161–1168, October 2021, 34556866, 10.1038/s41592-021-01254-9, 237616424, JOURNAL, 10.3390/genes13122280, 9777648, 36553546, free, Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice, 2022, Terrón-Camero, Laura C., Gordillo-González, Fernando, Salas-Espejo, Eduardo, Andrés-León, Eduardo, Genes, 13, 12, 2280, JOURNAL, 10.3389/fgene.2019.00614, 6609566, 31316552, free, Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines, 2019, Federico, Anthony, Karagiannis, Tanya, Karri, Kritika, Kishore, Dileep, Koga, Yusuke, Campbell, Joshua D., Monti, Stefano, Frontiers in Genetics, 10, 614, Scientific workflow systems like Nextflow allow formalizing an analysis as a data analysis pipeline. Pipelines, also known as workflows, are instructions that specify order and conditions of computing steps to be performed. They are carried out by special purpose programs, so-called workflow executors, which ensure predictable and reproducible behavior in various compute environments.JOURNAL, 10.1093/nar/gkac286, 9252820, 35536253, BioUML—towards a universal research platform, 2022, Kolpakov, Fedor, Akberdin, Ilya, Kiselev, Ilya, Kolmykov, Semyon, Kondrakhin, Yury, Kulyashov, Mikhail, Kutumova, Elena, Pintus, Sergey, Ryabova, Anna, Sharipov, Ruslan, Yevshin, Ivan, Zhatchenko, Sergey, Kel, Alexander, Nucleic Acids Research, 50, W1, W124–W131, JOURNAL, 10.1186/s12864-020-6714-x, 7168977, 32306927, Dolphin Next: A distributed data processing platform for high throughput genomics, 2020, Yukselen, Onur, Turkyilmaz, Osman, Ozturk, Ahmet Rasit, Garber, Manuel, Kucukural, Alper, BMC Genomics, 21, 1, 310, free, JOURNAL, 10.1093/nar/gkab346, 8218198, 33978761, The Dockstore: Enhancing a community platform for sharing reproducible and accessible computational protocols, 2021, Yuen, Denis, Cabansay, Louise, Duncan, Andrew, Luu, Gary, Hogue, Gregory, Overbeck, Charles, Perez, Natalie, Shands, Walt, Steinberg, David, Reid, Chaz, Olunwa, Nneka, Hansen, Richard, Sheets, Elizabeth, o'Farrell, Ash, Cullion, Kim, o'Connor, Brian D, Paten, Benedict, Stein, Lincoln, Nucleic Acids Research, 49, W1, W624–W632, Workflow systems also provide built-in solutions to common challenges of workflow development, such as the application to multiple samples, the validation of input and intermediate results, conditional execution of steps, error handling, and report generation. Advanced features of workflow systems may also include scheduling capabilities, graphical user interfaces for monitoring workflow executions, and the management of dependencies by containerizing the whole workflow or its components.JOURNAL, 10.1038/s41598-021-99288-8, 8569008, 34737383, Design considerations for workflow management systems use in production genomics research and the clinic, 2021, Ahmed, Azza E., Allen, Joshua M., Bhat, Tajesvi, Burra, Prakruthi, Fliege, Christina E., Hart, Steven N., Heldenbrand, Jacob R., Hudson, Matthew E., Istanto, Dave Deandre, Kalmbach, Michael T., Kapraun, Gregory D., Kendig, Katherine I., Kendzior, Matthew Charles, Klee, Eric W., Mattson, Nate, Ross, Christian A., Sharif, Sami M., Venkatakrishnan, Ramshankar, Fadlelmola, Faisal M., Mainzer, Liudmila S., Scientific Reports, 11, 1, 21680, 2021NatSR..1121680A, JOURNAL, 10.1186/s12859-018-2446-1, 6264621, 30486782, Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics, 2018, Baichoo, Shakuntala, Souilmi, Yassine, Panji, Sumir, Botha, Gerrit, Meintjes, Ayton, Hazelhurst, Scott, Bendou, Hocine, Beste, Eugene de, Mpangase, Phelelani T., Souiai, Oussema, Alghali, Mustafa, Yi, Long, o'Connor, Brian D., Crusoe, Michael, Armstrong, Don, Aron, Shaun, Joubert, Fourie, Ahmed, Azza E., Mbiyavanga, Mamana, Heusden, Peter van, Magosi, Lerato E., Zermeno, Jennie, Mainzer, Liudmila Sergeevna, Fadlelmola, Faisal M., Jongeneel, C. Victor, Mulder, Nicola, BMC Bioinformatics, 19, 1, 457, free, Typically, scientific workflow systems initially present a steep learning challenge as all their features and complexities are added on top of and in addition to the actual analysis. However, the standards and abstraction imposed by workflow systems ultimately improve the traceability of analysis steps, which is particularly relevant when collaborating on pipeline development, as is customary in scientific settings.JOURNAL, 10.1371/journal.pcbi.1008622, 7906312, 33630841, Using prototyping to choose a bioinformatics workflow management system, 2021, Jackson, Michael, Kavoussanakis, Kostas, Wallace, Edward W. J., PLOS Computational Biology, 17, 2, e1008622, 2021PLSCB..17E8622J, free,

Characteristics

Specification of workflows

In Nextflow, pipelines are constructed from individual processes that correspond to computational tasks. Each process is set up with input requirements and output declarations. Rather than running in a fixed succession, the execution of a process commences when all its input requirements are met. By specifying the output of one process as the input of another step, a logical and sequential connection between processes is created.JOURNAL, 10.1051/jbio/2017029, 29412134, Nextflow : Un outil efficace pour l'amélioration de la stabilité numérique des calculs en analyse génomique, 2017, Tommaso, Paolo Di, Floden, Evan W., Magis, Cedrik, Palumbo, Emilio, Notredame, Cedric, Biologie Aujourd'hui, 211, 3, 233–237, This reactive implementation of processes is a characteristic design pattern of Nextflow and also known as functional dataflow model.WEB, Nextflow Documentation - Channels,weblink 6 June 2022, docs.nextflow.io, It allows for the efficient parallelization of independent compute steps. Processes and whole workflows are programmed in a domain-specific language (DSL) that is provided by Nextflow and based on Apache Groovy.WEB, Nextflow Documentation - Domain Specific Language (DSL) 2,weblink 6 June 2022, docs.nextflow.io, While Nextflow's DSL is used to declare the workflow logic, developers can use their scripting language of choice within a process and mix multiple languages in a workflow. Porting existing scripts and workflows to Nextflow is therefore possible. Supported scripting languages include bash, csh, ksh, Python, Ruby, and R. Any scripting language that uses the standard Unix shebang declaration (#!/bin/bash) is supported in Nextflow.An exemplary workflow consisting of only one process is shown below:process hello_world {



}workflow { }To facilitate straightforward collaboration on workflows, Nextflow has native support for source-code management systems and DevOps-platforms including GitHub, GitLab, and others.WEB, Nextflow Documentation - Pipeline Sharing,weblink 6 June 2022, docs.nextflow.io,

Execution of workflows

Workflows written in Nextflow's DSL can be deployed and run across diverse computing environments without modifications to the pipeline code. To enable portability, Nextflow ships with dedicated executors for a variety of platformsWEB, Nextflow Documentation - Executors,weblink 6 June 2022, docs.nextflow.io, including those of major cloud providers. Because Nextflow decouples individual process steps, it can optionally be configured to spread execution across multiple computing platforms. It supports the following environments for pipeline execution:

• Local – the default executor. Nextflow pipelines run on Linux or Mac OS and execution occurs on the computer where the pipeline is launched.
• HPC workload managers – Slurm, SGE, LSF, Moab, PBS Pro, PBS/Torque, HTCondor, NQSII, OAR
• Kubernetes – local or cloud-based Kubernetes implementations (GKE, EKS, or AKS)
• Cloud batch services – AWS Batch,WEB, Nextflow Documentation - Amazon Cloud,weblink 6 June 2022, docs.nextflow.io, Azure BatchWEB, Nextflow Documentation - Azure Cloud,weblink 6 June 2022, docs.nextflow.io,
• Other environments – Apache Ignite, Google Life SciencesWEB, Nextflow Documentation - Google Cloud,weblink 6 June 2022, docs.nextflow.io,

Containers for portability across computing environments

A fundamental concept of Nextflow is its tight integration with software containers. Whole workflows and, in later versions, also single processes can harness containers to allow their execution across various compute environments without tedious installation and configuration routines.This design choice was strongly influenced by Solomon Hyke's talk at dotScale in 2013,WEB, Hykes, Solomon, 7 June 2013, Dot Scale 2013 - Why we built Docker,weblink 6 June 2022, YouTube, which had a significant impact on Nextflow's principal developer, Paolo Di Tommaso.WEB, Di Tomasso, Paolo, 14 October 2021, The story of Nextflow: Building a modern pipeline orchestrator,weblink 6 June 2022, eLifeSciences.org, Container frameworks supported by Nextflow include Docker, Singularity, Charliecloud, Podman, and Shifter.WEB, Nextflow Documentation - Containers,weblink 7 June 2022, docs.nextflow.io, Those type of containers can be utilized in a workflow and are automatically retrieved from external repositories when the pipeline is executed. At Nextflow Summit 2022, it was unveiled that future versions of Nextflow will support a dedicated container provisioning service for an improved integration of customized containers into workflows.WEB, Di Tommaso, Paolo, 13 October 2022, Nextflow and the future of containers,weblink 17 November 2022, YouTube,

Developmental history

Nextflow was originally developed at the Centre for Genomic Regulation in Spain and released as an open-source project on GitHub in July 2013.WEB, Release Version 0.3.0 · nextflow-io/nextflow,weblink 31 May 2022, GitHub, en, In October 2018, the project license for Nextflow was changed from GPLv3 to Apache 2.0.WEB, Di Tomasso, Paolo, 24 October 2018, Goodbye zero, Hello Apache!,weblink 7 June 2022, Nextflow.io/blog, In July 2018, Seqera Labs was launched as a spin-off from the Centre for Genomic Regulation. The company employs many of Nextflow's core developers and maintainers and provides commercial services WEB, Di Tommaso, Paolo, 8 October 2019, Introducing Nextflow Tower - Seamless monitoring of data analysis workflows from anywhere,weblink 7 June 2022, Seqera.IO, and consulting with a focus on Nextflow. In July 2020, a major extension and revision of Nextflow's domain-specific language was introduced to allow for sub-workflows and additional improvements.WEB, Di Tommaso, Paolo, 24 July 2020, Nextflow DSL 2 is here!,weblink 7 June 2022, Nextflow.IO/blog, In the same year, monthly downloads of Nextflow sat at approximately 55,000 per month.

Adoption and reception

The nf-core community

In addition to the Centre for Genomic Regulation,JOURNAL, Di Tomasso, Paolo, Chatzou, Maria, Floden, Evan, Prieto Barja, Pablo, Palumbo, Emilio, Notredame, Cedric, 11 April 2017, Nextflow enables reproducible computational workflows,weblink 7 June 2022, Nature Biotechnology, 35, 4, 316–319, 10.1038/nbt.3820, 28398311, 9690740, other sequencing facilities have adopted Nextflow as their preferred Scientific workflow system, among them the Quantitative Biology Center in Tübingen, the Francis Crick Institute, A*STAR Genome Institute of Singapore, and the Swedish National Genomics Infrastructure. Efforts to share, harmonize, and curate the bioinformatic pipelines used by those facilitiesJOURNAL, 10.7717/peerj.10947, 7977378, 33777521, Reproducible, portable, and efficient ancient genome reconstruction with nf-core/Eager, 2021, Fellows Yates, James A., Lamnidis, Thiseas C., Borry, Maxime, Andrades Valtueña, Aida, Fagernäs, Zandra, Clayton, Stephen, Garcia, Maxime U., Neukamm, Judith, Peltzer, Alexander, PeerJ, 9, e10947, free, JOURNAL, 10.1093/nargab/lqac007, 8808542, 35118380, Nf-core/Mag: A best-practice pipeline for metagenome hybrid assembly and binning, 2022, Krakau, Sabrina, Straub, Daniel, Gourlé, Hadrien, Gabernet, Gisela, Nahnsen, Sven, Nar Genomics and Bioinformatics, 4, lqac007, JOURNAL, 10.12688/f1000research.16665.2, 7111497, 32269765, Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants, 2020, Garcia, Maxime, Juhos, Szilveszter, Larsson, Malin, Olason, Pall I., Martin, Marcel, Eisfeldt, Jesper, Dilorenzo, Sebastian, Sandgren, Johanna, Díaz De Ståhl, Teresita, Ewels, Philip, Wirta, Valtteri, Nistér, Monica, Käller, Max, Nystedt, Björn, F1000Research, 9, 63, free, JOURNAL, 10.1186/s12859-022-05125-8, 9875403, 36694127, Nf-core/Circrna: A portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs, 2023, Digby, Barry, Finn, Stephen P., ó Broin, Pilib, BMC Bioinformatics, 24, 1, 27, free, eventually turned into the nf-core project.WEB, Ewels, Philip, Peltzer, Alexander, Fillinger, Sven, Alneberg, Johannes, Patel, Harshil, Wilm, Andreas, Garcia, Maxime Ulysse, Di Tommaso, Paolo, Nahnsen, Sven, April 1, 2019, Nf-core: Community curated bioinformatics pipelines,weblink June 30, 2022, Research Gate, Spearheaded by Phil Ewels from the Swedish National Genomics InfrastructureWEB, Zapata Garin, Claire-Alix, nf-core: a community-driven initiative to standardise Nextflow-based pipelines,weblink June 30, 2022, Lifebit.ai, WEB, February 14, 2020, The nf-core community provides computational pipelines,weblink June 30, 2022, SciLifeLab, the focus of the nf-core project is to ensure that pipelines are reproducible and portable across different hardware, operating systems, and software versions. In July 2020, Nextflow and nf-core were awarded a grant from the Chan Zuckerberg Initiative, recognizing its role as a vital open-source software.WEB, 27 July 2020, Nextflow and nf-core: Reproducible Workflows for the Scientific Community,weblink 15 June 2022, Chan Zuckerberg Initiative, As of 2022, the nf-core organization hosts 73 Nextflow pipelines for the biosciences and more than 700 process modules. Uniting more than 500 developers and scientists, it is the largest collaborative effort and community to develop bioinformatic data analysis pipelines.WEB, nf-core Github organization,weblink 18 November 2022, GitHub,

By domain and research subject

Nextflow is preferred in sequencing data processing and genomic data analysis. Over the last five years, numerous pipelines for many different applications and analyses in the field of genomics have been published.A notable use case in this regard was for pathogen surveillance during the COVID-19 pandemic.WEB, Floden, Evan, 5 November 2021, Genetic Sequencing Will Enable Us To Win The Global Battle Against COVID-19,weblink Monitoring the emergence of new virus variants and retracing its global spread required the swift and highly automatized, yet accurate, processing of raw data, variant analysis, and the designation of lineages, which was enabled by pipelines written in Nextflow.JOURNAL, 10.1093/cid/ciab785, 8634317, 34850839, Overcoming Data Bottlenecks in Genomic Pathogen Surveillance, 2021, Afolayan, Ayorinde O., Bernal, Johan Fabian, Gayeta, June M., Masim, Melissa L., Shamanna, Varun, Abrudan, Monica, Abudahab, Khalil, Argimón, Silvia, Carlos, Celia C., Sia, Sonia, Ravikumar, Kadahalli L., Okeke, Iruka N., Donado-Godoy, Pilar, Aanensen, David M., Underwood, Anthony, Harste, Harry, Kekre, Mihir, Muddyman, Dawn, Taylor, Ben, Wheeler, Nicole, David, Sophia, Arevalo, Alejandra, Fernanda Valencia, Maria, Osma Castro, Erik C D., Nagaraj, Geetha, Govindan, Vandana, Prabhu, Akshata, Sravani, D., Shincy, M. R., Rose, Steffimole, Clinical Infectious Diseases, 73, Suppl_4, S267–S274, 1, JOURNAL, 10.1371/journal.pone.0262953, 8791494, 35081137, free, ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants, 2022, Tilloy, Valentin, Cuzin, Pierre, Leroi, Laura, Guérin, Emilie, Durand, Patrick, Alain, Sophie, PLOS ONE, 17, 1, e0262953, 2022PLoSO..1762953T, JOURNAL, 10.1128/mSystems.00190-20, 7406220, 32753501, Bactopia: A Flexible Pipeline for Complete Analysis of Bacterial Genomes, 2020, Petit, Robert A., Read, Timothy D., mSystems, 5, 4, JOURNAL, 10.1128/msystems.00741-22, 9599279, 36069454, Meta Phage: An Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data, 2022, Pandolfo, Mattia, Telatin, Andrea, Lazzari, Gioele, Adriaenssens, Evelien M., Vitulo, Nicola, mSystems, 7, 5, e0074122, JOURNAL, 10.3390/biology11020263, 8868628, 35205129, free, Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis, 2022, Gauthier, Marie-Emilie A., Lelwala, Ruvini V., Elliott, Candace E., Windell, Craig, Fiorito, Sonia, Dinsdale, Adrian, Whattam, Mark, Pattemore, Julie, Barrero, Roberto A., Biology, 11, 2, 263, JOURNAL, 10.3389/fgene.2021.711437, 8355734, 34394197, free, Pore Cov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing, 2021, Brandt, Christian, Krautwurst, Sebastian, Spott, Riccardo, Lohde, Mara, Jundzill, Mateusz, Marquet, Mike, Hölzer, Martin, Frontiers in Genetics, 12, 711437, JOURNAL, 10.3390/genes13081330, 9394340, 35893066, free, A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains, 2022, Afiahayati, Bernard, Stefanus, Gunadi, Wibawa, Hendra, Hakim, Mohamad Saifudin, Marcellus, Parikesit, Arli Aditya, Dewa, Chandra Kusuma, Sakakibara, Yasubumi, Genes, 13, 8, 1330, Nextflow also plays an important role for the non-profit plasmid repository Addgene, which uses it to corroborate the integrity of all deposited plasmids.WEB, Niehaus, Jason, 14 July 2022, Bioinformatics at Addgene,weblink 25 February 2023, Addgene corporate blog, Apart from genomics, Nextflow is gaining popularity in other domains of biomedical data processing, which also require the application of complex workflows on large amounts of primary data: Drug screening,JOURNAL, 10.1093/bioadv/vbac089, 9722223, 36699347, Quasi Flow: A Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data, 2022, Ssekagiri, Alfred, Jjingo, Daudi, Lujumba, Ibra, Bbosa, Nicholas, Bugembe, Daniel L., Kateete, David P., Jordan, I King, Kaleebu, Pontiano, Ssemwanga, Deogratius, Bioinformatics Advances, 2, vbac089, Diffusion magnetic resonance imaging (dMRI) in radiology,JOURNAL, 10.1016/j.neuroimage.2020.116889, 32447016, Tracto Flow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity, 2020, Theaud, Guillaume, Houde, Jean-Christophe, Boré, Arnaud, Rheault, François, Morency, Felix, Descoteaux, Maxime, NeuroImage, 218, 116889, 164318811, free, and mass spectrometry data processing,JOURNAL, 10.1038/s41467-021-26214-x, 8501076, 34625563, Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry, 2021, Van Maldegem, Febe, Valand, Karishma, Cole, Megan, Patel, Harshil, Angelova, Mihaela, Rana, Sareena, Colliver, Emma, Enfield, Katey, Bah, Nourdine, Kelly, Gavin, Tsang, Victoria Siu Kwan, Mugarza, Edurne, Moore, Christopher, Hobson, Philip, Levi, Dina, Molina-Arcas, Miriam, Swanton, Charles, Downward, Julian, Nature Communications, 12, 1, 5906, 2021NatCo..12.5906V, JOURNAL, 10.1093/bioinformatics/btaa1093, 33416868, Diamond: A multi-modal DIA mass spectrometry data processing pipeline, 2021, Li, Chenxin, Gao, Mingxuan, Yang, Wenxian, Zhong, Chuanqi, Yu, Rongshan, Bioinformatics, 37, 2, 265–267, JOURNAL, 10.1093/bioinformatics/btac419, 35758608, TIMSCONVERT: A workflow to convert trapped ion mobility data to open data formats, 2022, Luu, Gordon T., Freitas, Michael A., Lizama-Chamu, Itzel, McCaughey, Catherine S., Sanchez, Laura M., Wang, Mingxun, Bioinformatics, 38, 16, 4046–4047, 9991885, the latter with a particular focus on proteomicsJOURNAL, 10.1002/pmic.201900147, 7613303, 31657527, Scalable Data Analysis in Proteomics and Metabolomics Using Bio Containers and Workflows Engines, 2020, Perez-Riverol, Yasset, Moreno, Pablo, Proteomics, 20, 9, e1900147, JOURNAL, 10.3390/genes12101645, 8535801, 34681040, free, FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow, 2021, Vlasova, Anna, Hermoso Pulido, Toni, Camara, Francisco, Ponomarenko, Julia, Guigó, Roderic, Genes, 12, 10, 1645, JOURNAL, 10.1186/s13059-022-02624-y, 8892804, 35241129, Enhanced protein isoform characterization through long-read proteogenomics, 2022, Miller, Rachel M., Jordan, Ben T., Mehlferber, Madison M., Jeffery, Erin D., Chatzipantsiou, Christina, Kaur, Simi, Millikin, Robert J., Dai, Yunxiang, Tiberi, Simone, Castaldi, Peter J., Shortreed, Michael R., Luckey, Chance John, Conesa, Ana, Smith, Lloyd M., Deslattes Mays, Anne, Sheynkman, Gloria M., Genome Biology, 23, 1, 69, free, JOURNAL, 10.3390/jpm12020263, 8875676, 35207751, free, SWAAT Bioinformatics Workflow for Protein Structure-Based Annotation of ADME Gene Variants, 2022, Othman, Houcemeddine, Jemimah, Sherlyn, Da Rocha, Jorge Emanuel Batista, Journal of Personalized Medicine, 12, 2, 263, JOURNAL, 10.1021/acs.jproteome.1c00123, 34153189, DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics, 2021, Bichmann, Leon, Gupta, Shubham, Rosenberger, George, Kuchenbecker, Leon, Sachsenberg, Timo, Ewels, Phil, Alka, Oliver, Pfeuffer, Julianus, Kohlbacher, Oliver, Röst, Hannes, Journal of Proteome Research, 20, 7, 3758–3766, 235597603,weblink free, JOURNAL, 10.1038/s41597-022-01380-9, 9197839, 35701420, Implementing the reuse of public DIA proteomics datasets: From the PRIDE database to Expression Atlas, 2022, Walzer, Mathias, García-Seisdedos, David, Prakash, Ananth, Brack, Paul, Crowther, Peter, Graham, Robert L., George, Nancy, Mohammed, Suhaib, Moreno, Pablo, Papatheodorou, Irene, Hubbard, Simon J., Vizcaíno, Juan Antonio, Scientific Data, 9, 1, 335, 2022NatSD...9..335W, JOURNAL, 10.1021/acs.jproteome.9b00328, 7116465, 31755270, ThermoRawFile Parser: Modular, Scalable, and Cross-Platform RAW File Conversion, 2020, Hulstaert, Niels, Shofstahl, Jim, Sachsenberg, Timo, Walzer, Mathias, Barsnes, Harald, Martens, Lennart, Perez-Riverol, Yasset, Journal of Proteome Research, 19, 1, 537–542, JOURNAL, 10.1002/pmic.201900334, 7718998, 32864883, Deep Rescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics, 2020, Li, Kai, Jain, Antrix, Malovannaya, Anna, Wen, Bo, Zhang, Bing, Proteomics, 20, 21–22, e1900334,

References

{{reflist}}

External links

• Official website
• nf-core project
• Seqera Labs

See also

GalaxySnakemake