Find out more at sarek: Introduction
Tuning pipeline performance (nf-core/bytesize #13) nf-core/bytesize: nf-core/airrflow
nf-core/rnaseq (nf-core/bytesize #32) This week, Maxime Garcia (@gau) will present Running pipelines offline. This will cover: - Using nf-core tools to download a
Buckle your seatbelts! We get to hear about the brand-new and shiny subworkflows that were introduced after the hackathon in This week, Gisela Gabernet (@ggabernet) will present: Pipeline code structure walkthrough. This talk will cover: * Talk through the Nextflow and nf-core Online Community Training - Session 4 (English) Session 4: March 16, 2023 - Configuration - Deployment
nf-core pipelines - Harshil Patel (Day 3_1) nf-core/coproid (nf-core/bytesize #29) nf-core/sarek is a pipeline designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse.
nf-core/hackathon March 2023: Welcome & Introduction nf-core/bytesize: gitpod.io
Nextflow & nf-core Online Community Training - Session 1 (English) nf-core/sarek: A workflow for germline, tumor-only, and somatic analysis of NGS data. Friederike Hanssen, Ph.D. Student at the I have downloaded sarek latest version using nf-core tools, with all singularity containers (in theory). When I move the pipeline to the cluster (no internet
This week, Payam Emami will present the nf-core/metaboigniter pipeline in a special edition of nf-core/bytesize focussed on Join us to hear Phil Ewels ( chat with Maxime Garcia ( and Franziska Bonath
Harshil Patel (@drpatelh) presents a Pipeline Code Structure walk through for the new DSL2 template. Find out more at Nextflow Summit 2022 - Friederike Hanssen nf-core/sarek: a comprehensive & efficient somatic & germline variant calling workflow. Friederike Hanssen, PhD candidate at the
'#23' by James Sarek Famke Bäuerle: Contributing to nf-core within a translational project for personalized Nextflow & nf-core Installation Made Easy!
nf-core/sarek: a pipeline for efficient germline, tumor-only, and somatic analysis of NGS data on different compute infrastructures This week, Friederike Hanssen (@FriederikeHanssen) presents how to use modules in a pipeline. This will cover: * Module file '#23' written and performed by James Sarek Filmed by Roger Allen, Marcel Glover, Tamara Draycott, Gavin Radcliffe Special
In this video, we explore a catalog of best-practice bioinformatic pipelines written in Nextflow available from the nf-core community Chris Wyatt shows us how to use GitPod ( for testing, development, and training. Here are some of the links and nf-core/bytesize: DSL2 coding style recommendations Part 1
Nextflow community meeting in South Korea (2nd) 세션 내용 [실습] Nextflow 기초 트레이닝 (핸즈온 세션) [이론] Sarek 워크플로우 DSL2: Pipeline Structure Walkthrough - Harshil Patel
nf-core tools & guidelines - Phil Ewels Find out more at Tutorial: Running pipelines:
Nextflow and nf-core Online Community Training - Session 3 (English) This week, Maxime Borry will present the nf-core/coproid pipeline in a special pipeline focused- episode on nf-core/bytesize Tutorial: running pipelines - Friederike Hanssen
nf-core/sarek is an established, comprehensive variant calling pipeline in the genomics field, which can be applied to any organism for which a reference genome Featured nf-core pipelines: Sarek - Maxime Garcia
nf-core/bytesize: A beginners guide to nf-core Nextflow and nf-core Hands-on Training A fast way to get up and running with Nextflow with hands-on training that is light on Command used and terminal output. $ nextflow run nf-core/sarek -r 3.4.2 -profile slurm,singularity --outdir sarek_GATK_hg38_output/ --input
Welcome to the March 2023 nf-core hackathon! This video kicks off the event and explains how to get started 00:00 Welcome nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any
In this video, I provide a high-level overview over different scRNA-Seq normalization methods. In particular, I discuss the Using the nf-core/sarek and nf-core/methylseq pipelines to analyse large clinical trial datasets. Eleanor Karp-Tatham, Postdoctoral nf-core/bytesize: nf-core/rnafusion (2022-09-13)
@Nextflow / @nf-core 2022 Training - Day 1 (Asia-Pacific) nf-core/sarek (nf-core/bytesize #28) Day 3 - session 1 Talk: nf-core pipelines - Harshil Patel | The Francis Crick Institute.
'#8' written and performed by James Sarek Filmed by Roger Allen, Marcel Glover, Tamara Draycott, Gavin Radcliffe Special Pipeline code walkthrough (nf-core/bytesize #3) sarek » nf-core
How to use modules in a pipeline (nf-core/bytesize #6a) nf-core/sarek: a pipeline for efficient germline - Friederike Hanssen - Poster - ISMB/ECCB 2023 Slurm crashes e.g. FASTP without informative error · Issue #1600 · nf
nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse. Nextflow and nf-core Hands-on Training
Unable to start · Issue #1725 · nf-core/sarek This week, Harshil Patel will present the nf-core/rnaseq pipeline in a special edition of nf-core/bytesize focussed on pipelines
Master Nextflow and nf-core installation in just a few minutes! This tutorial walks you through the complete setup process for I'm attempting to utilize the Sarek pipeline for analyzing Ion Torrent data, but I'm facing challenges with configuring single-end files.
Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species nf-core/bytesize: Special Interest Group - Animal Genomics
Gisela Gabernet talks about the newest developments in the nf-core/airrflow pipeline. nf-core/airrflow is a bioinformatics The nf-core Request for Comment (RFC) process is designed to give the community a voice and visibility to large projects that Nextflow and nf-core Online Community Training - Session 3 (English) Session 3: March 15, 2023 - Managing dependencies and
containers missing in nf-core download · Issue #769 · nf-core/sarek This week, Gisela Gabernet will present Tuning pipeline performance. This will cover: - Analysis of computational resource usage
nf-core/bytesize: nf-core/nanoseq Maxime Garcia talks about what to pay attention to when coding with DSL2. Adapting nf-core/sarek for Ion Torrent Single-End Data Analysis
@Nextflow / @nf-core 2022 Training - Day 1 (North, Central and South America) Yuk Kei Wan is talking about the functions of the nf-core/nanoseq pipeline. More information about the pipeline can be found This week, José Fernandez will present the nf-core/sarek pipeline in a very special episode of nf-core/bytesize talks focused on
nf-core/ampliseq (nf-core/bytesize #25) Franziska Bonath shares her experiences as a beginner of using nf-core provided material and will give tips on how to get started.
Nextflow Summit Boston 2023 - Eleanor Karp-Tatham Nextflow 기초실습 및 nf-core/sarek 소개
One of our first bytesize talks described the use of nf-core configs in the context of nf-core pipelines. In an extension to this nf-core/metaboigniter (nf-core/bytesize #26) This week, Maxime Garcia (@MaxUlysse) will present: How nf-core configs work. This talk will cover: * Making your own Nextflow
@Nextflow / @nf-core 2022 Training - Day 1 (Europe, the Middle East, and Africa) nf-core/sarek: Analysis pipeline to detect germline or - GitHub Episode 40: Origins of nf-core - SciLifeLab NGI
Running pipelines offline (nf-core/bytesize #8) nf-core/bytesize: nf-core/cutandrun
Normalization methods for single-cell RNA-Seq data (high-level overview) '#8' by James Sarek
Nextflow Summit Boston 2023 - Maxime Garcia This week, Evan Floden will present the Nextflow Tower CLI during as part of the nf-core/bytesize series. nf-core presents bytesize
nfcore/sarek - Docker Image nf-core/bytesize: integrate custom scripts in Nextflow pipelines Nextflow Tower CLI (nf-core/bytesize #33)
Nextflow Summit 2023 - Friederike Hanssen Nextflow Tutorial #4: Exploring nf-core pipelines
First of all, congrats and thanks for your work. I am new to the Nextflow/nf-core field and I am trying to run the pipeline This week, Daniel Straub will present the nf-core/ampliseq pipeline in a special edition of nf-core/bytesize focussed on pipelines. nf core bytesize rfcs
nf-core/bytesize: nf-core Subworkflows In this week's bytesize, Cedric Notredame, Björn Lange, Francesca Bernini and Jose Espinosa-Carrasco are introducing the Scalable and efficient DNA sequencing analysis on different
Annick Renevey is explaining the nf-core/rnafusion pipeline in this weeks bytesize talk. Find out more at nf-core/sarek - Reproducible Bioinformatics Workflows with Nextflow
Featured nf-core pipelines: viralrecon - Harshil Patel nf-core/sarek - evolution of a community pipeline started in 2016 Maxime Garcia, Bioinformatician at Seqera. From the Nextflow and nf-core Online Community Training - Session 4 (English)
Live stream of Nextflow and nf-core training. Please post questions on Slack: nf-core/bytesize: Using nf-core configs in custom pipelines Nextflow and nf-core Online Community Training - Session 1 Session 1: March 13, 2023 - Welcome - An introduction to Nextflow
Contributing to nf-core within a translational project for personalized cancer medicine in Germany Famke Bäuerle - PhD Student, Chris Hakkaart shows how custom scripts, such as R or Perl o Python scripts, can be integrated into a Nextflow pipeline. How nf-core configs work (nf-core/bytesize #2)