- 229
- 132 527
Nextflow
Spain
Registrace 22. 12. 2015
Welcome to the Nextflow workflow manager channel!
Episode 42: Nextflow on the Road — ISMB 2024 in Montreal
Our small but intrepid team of Seqerans recently attended the ISMB 2024 conference in Montreal, a great mix of computational biology and bioinformatics with a largely academic / research-focused audience. Join Geraldine Van der Auwera, Rob Syme and Florian Wuennemann for a lively discussion about the scientific themes of the conference, their experience running the booth, meeting with the ISMB and BOSC community, and resources for job seekers.
zhlédnutí: 28
Video
Episode 41: New syntax in Nextflow 24.04
zhlédnutí 146Před 14 dny
Phil Ewels and Ben Sherman from Seqera discuss the latest Nextflow 24.04 release. This episode focuses on the new "workflow output definition", showcasing how it simplifies and centralizes the publishing process in Nextflow pipelines. They also touch on the new syntax features like topic channels, eval outputs, job arrays and support for GA4GH TES and Singularity OCI. We'd really hoping for Nex...
Episode 43: Data Studios
In this episode we explore the new features of Seqera's Data Studios and Data Explorer, with Phil Ewels, Rob Newman and Rob Syme from Seqera. Discover how to use these tools for troubleshooting Nextflow pipelines, tertiary analysis and Nextflow development. We discuss the pain points that led to the creation of Data Studios and how it's designed to allow scientists to interactively and collabor...
Podcast Episode 41 Highlight: Workflow output definition
zhlédnutí 74Před 21 dnem
Short clip from the upcoming Channels Podcast, Episode 41. We talk about the Workflow Output Definition, which will replace publishDir. We want your feedback! Watch the full podcast episode for more details.
Episode 40: Origins of nf-core - SciLifeLab NGI
zhlédnutí 33Před měsícem
Join us to hear Phil Ewels ( tallphil) chat with Maxime Garcia ( gau) and Franziska Bonath ( FranBonath) about how nf-core started at the National Genomics Infrastructure (NGI) at SciLifeLab in Sweden. We chat about how the nf-core/sarek (nf-co.re/sarek) pipeline grew alongside and eventually joined nf-core, as well as the early days of nf-core bytesize talks an...
Episode 39: Spatial proteomics at Pixelgen
zhlédnutí 87Před měsícem
Tune in to hear all about Pixelgen Technologies - creators of a novel technology for doing single-cell spatial proteomics. We chat about how this fascinating technology works, what you can do with the data and why they chose to develop their analysis suite as an open-source nf-core pipeline. Links: - Software: - nf-core/pixelator pipeline: nf-co.re/pixelator - Pixelator Python package: github.c...
Episode 38: Seqera Pipelines & Seqera Containers
zhlédnutí 147Před měsícem
Evan Floden (CEO and co-founder of Seqera) joins Phil Ewels (Product Manager for OSS at Seqera) to talk about two of the big announcements at the recent Nextflow Summit Boston 2024 - Seqera Pipelines and Seqera Containers. We dive into what these two new community offerings are, why we built them and how they work. Links: - seqera.io/pipelines/ - seqera.io/containers/ - Blog post: seqera.io/blo...
Zachary Charlop-Powers: Nextflow In Synthetic Biology and Natural Product Discovery
zhlédnutí 193Před měsícem
Zachary Charlop-Powers Computational scientist at Ginkgo Bioworks Recap of the power and challenges of using NextFlow for bioinformatic workflow creation across three different companies in the (meta-) genome and synbio space. Nextflow Summit - Boston 2024 summit.nextflow.io/2024/boston/agenda/05-24 nextflow-in-synthetic-biology-and/
Jeffrey Zhou: Using Nextflow to Orchestrate Tightly-coupled HPC Workloads on Rescale
zhlédnutí 81Před 2 měsíci
Jeffrey Zhou Director of Product Management at Rescale Many of the principles of nextflow such as separation of execution environment and code, the dataflow paradigm, and its ability to work with multiple tools are relatively new to fields that are used to submitting a few tightly coupled HPC jobs in an on-premise cluster using a job scheduler. However, with an increased emphasis on using cloud...
Panel Discussion: Diversifying the pipeline: Fostering first-gen success in biotech
zhlédnutí 109Před 2 měsíci
Geraldine Van der Auwera Lead Developer Advocate at Seqera Edgardo Sanabria-Valentín Associate Program Director of PRISM at John Jay College, CUNY Irina Silva Field Marketing and Alliances at Seqera Lyndon Mitnaul Senior Director, Regeneron Genetics Center We all know the workforce in US biotech today is far from representative of the US population. This panel will focus on one critical dimensi...
Corrie Painter: Breaking Bad Barriers: Overcoming challenges in Rare Cancer Research and Innovation
zhlédnutí 59Před 2 měsíci
Corrie Painter VP of External Research and Partnerships at Precede Biosciences Despite rare cancers accounting for 25% of adult tumors, they are difficult to study due to the low disease incidence and geographically dispersed patient populations, which has resulted in significant unmet clinical needs for patients with rare cancers. The Broad Institute of MIT and Harvard launched a series of gen...
Nils Homer: Fastquorum: the fgbio best-practices for UMI-based consensus calling from raw FASTQs
zhlédnutí 262Před 2 měsíci
Nils Homer Founding Partner of Fulcrum Genomics Fastquorum is a nf-core Nextflow pipeline to produce UMI-based consensus sequencing reads from raw FASTQs for powerful error-correction to improve sequencing adapters. Individual library molecules are tagged with unique molecular identifiers (UMIs) prior to amplification, such that multiple observations of each library molecule can be made. In som...
Rob Syme: Practical Data Studios
zhlédnutí 228Před 2 měsíci
Rob Syme Scientific Support Lead at Seqera Interactive analysis and visualization of outputs from secondary data analysis, such as genomic alignments, variant calls, single-cell quantifications, or microscopy images is critical for biological interpretation and to confirm or refute experimental hypotheses. Data Studios is a new feature on the Seqera Platform where you can host a combination of ...
Colby T. Ford: Building Enterprise-Grade Bioinformatics Pipelines using Cloud-Scale Kubernetes
zhlédnutí 121Před 2 měsíci
Colby T. Ford Principal Consultant at Tuple - The Cloud Genomics Company, Author of "Genomics in the Azure Cloud" (O'Reilly, 2022) Workflow tools like Nextflow allow us to standardize and automate our bioinformatics pipelines. Coupled with Docker and Kubernetes, our pipelines then become portable and scalable. In this session, we will take a deep dive into the world of cloud-based Kubernetes an...
Angel Pizarro: What to know about and where to look for it when running Nextflow on the cloud
zhlédnutí 98Před 2 měsíci
Angel Pizarro Principal Developer Advocate for AWS Batch Deploying Nextflow workflows on the cloud is just one part of the overall developer and operating experience. In this session, we'll take a deep dive into infrastructure considerations to help you maximize the price and performance of running your workflows on AWS. Nextflow Summit - Boston 2024 summit.nextflow.io/2024/boston/agenda/05-24 ...
Andrew Stiles: Static Code Analysis of Nextflow Pipelines
zhlédnutí 79Před 2 měsíci
Andrew Stiles: Static Code Analysis of Nextflow Pipelines
Alvaro Martinez Barrio: Nextflow allows Pixelgen innovation engine to reach the market quicker
zhlédnutí 94Před 2 měsíci
Alvaro Martinez Barrio: Nextflow allows Pixelgen innovation engine to reach the market quicker
Jonathon Keeney: Introduction to BioCompute and Integration with Nextflow
zhlédnutí 124Před 2 měsíci
Jonathon Keeney: Introduction to BioCompute and Integration with Nextflow
Vlad Savelyev: MultiQC: meet Plotly and notebooks
zhlédnutí 109Před 2 měsíci
Vlad Savelyev: MultiQC: meet Plotly and notebooks
Paolo Di Tommaso: What's new in the Nextflow ecosystem
zhlédnutí 186Před 2 měsíci
Paolo Di Tommaso: What's new in the Nextflow ecosystem
Sateesh Peri: Cloud Empowerment: Unleashing the Potential of Memory Machine Cloud Snapshot Engine
zhlédnutí 74Před 2 měsíci
Sateesh Peri: Cloud Empowerment: Unleashing the Potential of Memory Machine Cloud Snapshot Engine
Brenna Novotny: SpaFlow: A Nextflow pipeline for single cell phenotyping in spatial omics
zhlédnutí 152Před 2 měsíci
Brenna Novotny: SpaFlow: A Nextflow pipeline for single cell phenotyping in spatial omics
Lorena Pantano: Transitioning through the nf-core era at the Harvard Chan Bioinformatics Core
zhlédnutí 76Před 2 měsíci
Lorena Pantano: Transitioning through the nf-core era at the Harvard Chan Bioinformatics Core
Alex V Caron: Mining diamonds with wooden hammers: getting diffusion MRI into the age of steel
zhlédnutí 94Před 2 měsíci
Alex V Caron: Mining diamonds with wooden hammers: getting diffusion MRI into the age of steel
Jason Fan: Get into the Groovy: using Groovy to model sample sheets, input and metadata, and more
zhlédnutí 176Před 2 měsíci
Jason Fan: Get into the Groovy: using Groovy to model sample sheets, input and metadata, and more
Andres Fernandez Benevento: Developing bioinformatic pipelines and sharing with nf-core
zhlédnutí 259Před 2 měsíci
Andres Fernandez Benevento: Developing bioinformatic pipelines and sharing with nf-core
Geraldine Van der Auwera: Community updates
zhlédnutí 61Před 2 měsíci
Geraldine Van der Auwera: Community updates
Evan Floden: Making scientific software accessible to all
zhlédnutí 148Před 2 měsíci
Evan Floden: Making scientific software accessible to all
Cool update! Thanks for the thorough explanation of the changes in this release. The editing on this episode is a bit heavy-handed, though. All of the cuts are a bit jarring to listen to and watch.
Congrats! Nice talk!
Great talk, Lorena! Thanks. We were 'bcbio' users at Iowa for a long time as well, but are switching to NF-core now.
I absolutely love it and I wish I knew more resources to learn more about nextflow.
Thanks for organizing these amazing talks @Nextflow
Apologies, Zoom had a hiccup and reset the streaming URL. Part 2 can be found here: czcams.com/users/liveLtEEsl4a2bE
Looking forward to attending the one in Boston!
Thanks for an excellent talk! I think I got some stuff to chip in about the provenance tracking, but will get back about that separately.
😻 Promo-SM
I just discovered Lorena, she is a superstar, what an inspiration!
Hi, could you share please the statics about women?
Thanks for putting all these talks online !
Everytime I think: "It would be realy nice if Nextflow could do this", someone in the NF-Core comunity comes along and implements something like it. Great Work!
I like the "channels" name!
Amazing presentation and pipeline idea!
First.
I'm using nextflow version 21.10.6, but the following error still appeared, i.e., "Channel read_pairs_ch has been used twice as an input by process fastqc and process quantification." Is there something that needs to be declared so the limitation that's supposed to be fixed can be used?
thanks a lot for sharing such valuable videos.
What does on tower mean?
Hi, Thanks for the great tutorial! I've got a question related to the sanity checks (35 min of the view). Let's assume that I don't have a paired file for the liver (so my input is: liver_1.fa, gut_1.fa, gut_2.fa, lung_1.fa, lung_2.fa) how to deal with it? Will it just generate an output without the liver samples?
Suuuuper cool wow. Will make my life soooo much easier. Thanks Evan & the nextflow team!
Wow. Goodbye every other cli workflow system
Hello, thank you for the nice video! I just got a problem when running script2.nf "-with-docker". The error message is "Unable to find image 'nextflow/rnaseq-nf:latest' locally". Would you suggest me how to fix it?
The container location has changed due to DockerHub policy. Use `-with-docker quay.io/nextflow/rnaseq-nf:latest`
@@evfloable Thanks! But it's still not working if I am not mistaken
@@bichngoccaotran1109 OK. Head over to gitter.im/nextflow-io/nextflow, provide some more details and someone from the community should be able to help out.
@@evfloable Thanks a lot, it does work now. I am a fan Wish one day we will have a Nextflow cheatsheet though!
Where can we find the training materials? I tried to reach www.seqera.io/training/ but there's nothing like what you're showing in the video.
seqera.io/training/
Thanks for the video. Can I please know if I can get the access to AWS environment showed in video and training material copy
Video doesn't really start until czcams.com/video/8_i8Tn335X0/video.html
Excellent introduction!
Must watch for every Bioinformatician!
Could you share the slides, please