As the field of genomics matures and new methodologies produce increasing quantities of data, new tools are needed to facilitate high-throughput analysis of large genomics datasets. Workflow managers are needed to handle automated workflows, able to dynamically launch and manage the chaining of numerous bioinformatics tools for hundreds of samples. Of these, Nextflow (https://nextflow.io, Tommaso et. al. Nat Biotech, 2017) has gained a large community and has become the industry standard for research groups and facilities. To help to standardise the bioinformatics results of different sequencing facilities and research groups, nf-core was formed to help scientists to collaborate on workflows (https://nf-co.re/, Nature Biotechnology 38, 276–278 (2020)). A community-led worldwide collaboration, the aim is to collect high-quality workflows that adhere to a strict set of standards and guidelines, leading to pipelines that are usable, maintainable and upgradeable.
External link for nf-core
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Are you interested in #nfcore #nextflow #pipelines ? 🐛 Need help setting up a pipeline or debug a run? 🦆 Developing an nf-core pipeline and need rubber-ducking of an issue? 🗣️ Connect to the nf-core weekly helpdesk for some face-to-face help with community experts! The last EMEA timezone session will take place today at 10:00 CET (Berlin time) on the nf-core gather.town (just need your browser): https://lnkd.in/dFWUtbzJ
Are you interested in #nfcore #nextflow #pipelines ? 🐛 Need help setting up a pipeline or debug a run? 🦆 Developing an nf-core pipeline and need rubber-ducking of an issue? 🗣️ Connect to the nf-core weekly helpdesk for some face-to-face help with community experts! The last EMEA timezone session will take place today at 10:00 CET (Berlin time) on the nf-core gather.town (just need your browser): https://lnkd.in/dFWUtbzJ
Our next hackathon is rapidly approaching! 🚀 - March 24-26, 2025 - Online / local distributed sites For the distributed sites, WE NEED YOU! 🎯 If you're able to book a meeting room and host a local site, fill in the local site registration form: https://lnkd.in/dApQA_aK Local sites can be any size, previously we've had numbers ranging from 4-80 people at a given site. So even if it's just you and your mates please do let us know! 🥳 The hackathon is loads of fun - last year it even inspired a song! https://lnkd.in/dKBurNkp Registration for the hackathon itself will open in mid-late January, so please get those sites registered ASAP so that we can include them in the event registration. If you have any questions, let us know on the nf-core Slack 😊 Let's get that map covered in pins! 🌎📍
Pipeline release! nf-core/methylseq v3.0.0 🎉 * Modular Bismark & Bwameth Subworkflows * GPU Support for Bwameth * BS-Seq Primer & Updated Documentation * Run Qualimap & Preseq Options * Reorganized Configuration Files See the changelog for details: https://lnkd.in/dKj47Uf3
Are you interested in #nfcore #nextflow #pipelines ? 🐛 Need help setting up a pipeline or debug a run? 🦆 Developing an nf-core pipeline and need rubber-ducking of an issue? 🗣️ Connect to the nf-core weekly helpdesk for some face-to-face help with community experts! Today's session will take place at 10:00 CET (Berlin time) on the nf-core gather.town (just need your browser): https://lnkd.in/dFWUtbzJ
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Seen an incredible influx of folks to 🦋 #Bluesky over the past few weeks - suddenly my feed there reminds me of happier #ScienceTwitter times. If you'd like to join the conversation there, check out the starter packs being curated by Stephen Turner - it's a great way to get kickstarted, and there's even a #Nextflow pack: https://lnkd.in/dscR4WCb If that's not enough, Edmund Miller is also curating a similar #Nextflow list at https://lnkd.in/d6ccf8fV - plenty to fill those feeds! 🎉
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Professor for Biomedical Data Science, Eberhard Karls Universität Tübingen & Director, Quantitative Biology Center (QBiC), Tübingen
On our new paper, we illustrate the benefits of using the nf-core best practices for pangenome graph construction. Great work by Simon Heumos , Michael Heuer Friederike Hanssen Lukas Heumos Andrea Guarracino Peter Heringe Philipp Ehmele Piotr Prins and Erik Garrison
All #NextflowSummit talks from last week are now online on YouTube! Check out the playlist below, there are lots from folks in the nf-core community! 🎉
Missed the #NextflowSummit in Barcelona last week? Don't worry, all the talks are now available on YouTube! 🎉 Check them out below 👇 https://hubs.ly/Q02WNhNK0 #NextflowSummit
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PhD student in the Schapiro group at the Institute for Computational Biomedicine | Nextflow ambassador
I had an amazing time at this week's #NextflowSummit and nf-core #hackathon in Barcelona. It is always exciting to see how people utilize Nextflow to push boundaries. It was a pleasure to lead the imaging pipelines group at the nf-core hackathon, where we worked on adding new tools into the nf-core framework and expanding the functionalities of multiplexed imaging pipelines. It was inspiring to see how much the interest in spatial technologies has grown since last year. I also presented a poster on our effort of bringing highly multiplexed imaging pipelines to nf-core, featuring nf-core/molkart (https://lnkd.in/emdkztgs) for processing targeted spatial transcriptomic data (MERSCOPE, Molecular Cartography) and the integration and expansion of MCMICRO (https://mcmicro.org/) into nf-core (https://lnkd.in/eZyXxjFG). You can view the poster here and feel free to reach out either on Slack or Github: https://lnkd.in/efS_Ce_J Thanks to everyone I met for making this such an insightful, productive and fun experience. Let’s keep the conversation going on best practices for spatial omics data processing! 🚀 #Nextflow, nf-core, Seqera
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🚀 This week, I had an amazing experience in Barcelona at the nf-core hackathon and #NextflowSummit! The first part of the week was all about teamwork, where we collaborated on the nf-core #scdownstream pipeline and contributed some important scverse tools for ambient RNA removal and doublet detection to nf-core/modules. Then, I wrapped up the week by attending great talks and workshops at the Nextflow Summit. 💡 A huge thank you to my hackathon team for the great collaboration and to the Nextflow Summit organizers for putting together such a fantastic event! 🙌🎉#nextflow #bioinformatics #nfcore #scverse #hackathon #conference #summit #seqera