nf-core/cnvflow: A Robust Nextflow Pipeline for Reproducible CNV Detection from Exome Data

nf-core/cnvflow: A Robust Nextflow Pipeline for Reproducible CNV Detection from Exome Data | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article nf-core/cnvflow: A Robust Nextflow Pipeline for Reproducible CNV Detection from Exome Data Nicholas Kwasi-Do Ohene Opoku, Henry Martin, Peter Amoako-Yirenkyi, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8713056/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Copy number variation (CNV) analysis plays a vital role in uncovering genomic alterations linked to disease. However, CNV detection workflows remain fragmented and often lack reproducibility. We present nf-core/cnvflow, a robust and reproducible Nextflow-based pipeline designed for read-depth-based CNV detection from exome data. The pipeline integrates four established CNV tools (CNVkit, CLAMMS, CoNIFER, and CONTRA) and supports containerized execution with Docker or Singularity. It accommodates diverse computing environments and includes automated quality control, coverage normalization, and tool-specific outputs. Benchmarking with 1000 Genomes Project data demonstrated its scalability and performance. nf-core/cnvflow provides a portable and extensible solution for standardized CNV analysis and is available under the nf-core community framework. Copy Number Variation NextFlow CLAMMS CNVKIT CoNIFER CONTRA Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8713056","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":591493518,"identity":"4c2cd644-2dff-46ae-bc1a-e83ea5d0e7ed","order_by":0,"name":"Nicholas Kwasi-Do Ohene Opoku","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA4klEQVRIiWNgGAWjYDACZgY2BoYCBgZ+BsYGEB9EshGhxYCBQbKBaC0MUC0GByA8wlrM2ZmfPfhgYGdvfPxw68YfDDayGw6wX3uAT4tlM5u54QyD5MRtZxLbbvMwpBlvOMBTboBPi8FhHjZpHgPmBLMDQC0MDIcTgVrSJIjQUm9v3P+w7eYPhv9EaznMuEEise0GD8MBoBb2YwS0sJlJzjA4njjjxkOgXwySjWcCDcGv5fzhZxIfKqrt+fvTn938UWEn23e8/RleLegmADEzD94AwwrYH5CsZRSMglEwCoY1AAC7X0j+fl4u/gAAAABJRU5ErkJggg==","orcid":"","institution":"Kwame Nkrumah University of Science and Technology","correspondingAuthor":true,"prefix":"","firstName":"Nicholas","middleName":"Kwasi-Do Ohene","lastName":"Opoku","suffix":""},{"id":591493521,"identity":"78751f20-ff2e-4f7a-bcb2-33e62195f3ba","order_by":1,"name":"Henry Martin","email":"","orcid":"","institution":"Kwame Nkrumah University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Henry","middleName":"","lastName":"Martin","suffix":""},{"id":591493522,"identity":"14e76c6a-5c55-45f4-9f91-d78665da4fb3","order_by":2,"name":"Peter Amoako-Yirenkyi","email":"","orcid":"","institution":"Kwame Nkrumah University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Peter","middleName":"","lastName":"Amoako-Yirenkyi","suffix":""},{"id":591493523,"identity":"aa4f1c14-289c-4b5d-a5ed-58870d1ce299","order_by":3,"name":"Samson Pandam Salifu","email":"","orcid":"","institution":"Kwame Nkrumah University of Science and Technology","correspondingAuthor":false,"prefix":"","firstName":"Samson","middleName":"Pandam","lastName":"Salifu","suffix":""}],"badges":[],"createdAt":"2026-01-27 17:09:42","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8713056/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8713056/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":103578829,"identity":"a4df03db-c51e-47ba-ac7b-889458bb45ae","added_by":"auto","created_at":"2026-02-27 09:43:17","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":320377,"visible":true,"origin":"","legend":"","description":"","filename":"RevisednfcorecnvflowManuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8713056/v1_covered_43d69016-85bb-4d53-ac4d-3ed7bb71fd1f.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"nf-core/cnvflow: A Robust Nextflow Pipeline for Reproducible CNV Detection from Exome Data","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Copy Number Variation, NextFlow, CLAMMS, CNVKIT, CoNIFER, CONTRA","lastPublishedDoi":"10.21203/rs.3.rs-8713056/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8713056/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Copy number variation (CNV) analysis plays a vital role in uncovering genomic alterations linked to disease. 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