Nextflow Summit 2023 - Friederike Hanssen containers missing in nf-core download · Issue #769 · nf-core/sarek nf-core/sarek - evolution of a community pipeline started in 2016 Maxime Garcia, Bioinformatician at Seqera. From the
@Nextflow / @nf-core 2022 Training - Day 1 (North, Central and South America) This week, Maxime Borry will present the nf-core/coproid pipeline in a special pipeline focused- episode on nf-core/bytesize
nf-core/bytesize: nf-core/airrflow I'm attempting to utilize the Sarek pipeline for analyzing Ion Torrent data, but I'm facing challenges with configuring single-end files.
Scalable and efficient DNA sequencing analysis on different Command used and terminal output. $ nextflow run nf-core/sarek -r 3.4.2 -profile slurm,singularity --outdir sarek_GATK_hg38_output/ --input
Nextflow & nf-core Online Community Training - Session 1 (English) Yuk Kei Wan is talking about the functions of the nf-core/nanoseq pipeline. More information about the pipeline can be found Featured nf-core pipelines: viralrecon - Harshil Patel
nf-core/sarek: a pipeline for efficient germline, tumor-only, and somatic analysis of NGS data on different compute infrastructures nf-core/bytesize: nf-core/rnafusion (2022-09-13) @Nextflow / @nf-core 2022 Training - Day 1 (Asia-Pacific)
Maxime Garcia talks about what to pay attention to when coding with DSL2. nf-core/bytesize: gitpod.io Harshil Patel (@drpatelh) presents a Pipeline Code Structure walk through for the new DSL2 template. Find out more at
Tuning pipeline performance (nf-core/bytesize #13) Master Nextflow and nf-core installation in just a few minutes! This tutorial walks you through the complete setup process for Adapting nf-core/sarek for Ion Torrent Single-End Data Analysis
Nextflow and nf-core Online Community Training - Session 4 (English) Find out more at This week, Maxime Garcia (@MaxUlysse) will present: How nf-core configs work. This talk will cover: * Making your own Nextflow
nf-core/bytesize: nf-core/nanoseq 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 nf-core/sarek: a pipeline for efficient germline - Friederike Hanssen - Poster - ISMB/ECCB 2023
Running pipelines offline (nf-core/bytesize #8) The nf-core Request for Comment (RFC) process is designed to give the community a voice and visibility to large projects that Welcome to the March 2023 nf-core hackathon! This video kicks off the event and explains how to get started 00:00 Welcome
Using the nf-core/sarek and nf-core/methylseq pipelines to analyse large clinical trial datasets. Eleanor Karp-Tatham, Postdoctoral 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 nf-core/bytesize: nf-core/cutandrun
In this video, I provide a high-level overview over different scRNA-Seq normalization methods. In particular, I discuss the Normalization methods for single-cell RNA-Seq data (high-level overview) Nextflow Summit 2022 - Friederike Hanssen
How to use modules in a pipeline (nf-core/bytesize #6a) nf-core/hackathon March 2023: Welcome & Introduction 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/sarek - Reproducible Bioinformatics Workflows with Nextflow 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
nf-core/sarek: Analysis pipeline to detect germline or - GitHub Nextflow and nf-core Online Community Training - Session 4 (English) Session 4: March 16, 2023 - Configuration - Deployment
nf-core/sarek: a comprehensive & efficient somatic & germline variant calling workflow. Friederike Hanssen, PhD candidate at the nf-core/bytesize: Using nf-core configs in custom pipelines Nextflow Tutorial #4: Exploring nf-core pipelines
Episode 40: Origins of nf-core - SciLifeLab NGI nfcore/sarek - Docker Image
Nextflow Tower CLI (nf-core/bytesize #33) '#23' by James Sarek Nextflow and nf-core Online Community Training - Session 3 (English)
nf core bytesize rfcs nf-core/bytesize: Special Interest Group - Animal Genomics Slurm crashes e.g. FASTP without informative error · Issue #1600 · nf
nf-core/bytesize: integrate custom scripts in Nextflow pipelines Franziska Bonath shares her experiences as a beginner of using nf-core provided material and will give tips on how to get started. This week, Gisela Gabernet will present Tuning pipeline performance. This will cover: - Analysis of computational resource usage
Famke Bäuerle: Contributing to nf-core within a translational project for personalized 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 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
This week, Harshil Patel will present the nf-core/rnaseq pipeline in a special edition of nf-core/bytesize focussed on pipelines Nextflow and nf-core Online Community Training - Session 3 (English) Session 3: March 15, 2023 - Managing dependencies and
'#23' written and performed by James Sarek Filmed by Roger Allen, Marcel Glover, Tamara Draycott, Gavin Radcliffe Special @Nextflow / @nf-core 2022 Training - Day 1 (Europe, the Middle East, and Africa) This week, Payam Emami will present the nf-core/metaboigniter pipeline in a special edition of nf-core/bytesize focussed on
In this video, we explore a catalog of best-practice bioinformatic pipelines written in Nextflow available from the nf-core community Day 3 - session 1 Talk: nf-core pipelines - Harshil Patel | The Francis Crick Institute.
Contributing to nf-core within a translational project for personalized cancer medicine in Germany Famke Bäuerle - PhD Student, nf-core tools & guidelines - Phil Ewels nf-core/sarek: A workflow for germline, tumor-only, and somatic analysis of NGS data. Friederike Hanssen, Ph.D. Student at the
Nextflow Summit Boston 2023 - Maxime Garcia '#8' by James Sarek Pipeline code walkthrough (nf-core/bytesize #3)
DSL2: Pipeline Structure Walkthrough - Harshil Patel sarek: Introduction nf-core/metaboigniter (nf-core/bytesize #26)
nf-core/coproid (nf-core/bytesize #29) Find out more at Tutorial: Running pipelines: Tutorial: running pipelines - Friederike Hanssen
Featured nf-core pipelines: Sarek - Maxime Garcia Annick Renevey is explaining the nf-core/rnafusion pipeline in this weeks bytesize talk. Find out more at
This week, Friederike Hanssen (@FriederikeHanssen) presents how to use modules in a pipeline. This will cover: * Module file nf-core pipelines - Harshil Patel (Day 3_1) nf-core/bytesize: A beginners guide to nf-core
Nextflow 기초실습 및 nf-core/sarek 소개 This week, Evan Floden will present the Nextflow Tower CLI during as part of the nf-core/bytesize series. nf-core presents bytesize How nf-core configs work (nf-core/bytesize #2)
Nextflow and nf-core Hands-on Training This week, Daniel Straub will present the nf-core/ampliseq pipeline in a special edition of nf-core/bytesize focussed on pipelines. Gisela Gabernet talks about the newest developments in the nf-core/airrflow pipeline. nf-core/airrflow is a bioinformatics
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 Nextflow and nf-core Online Community Training - Session 1 Session 1: March 13, 2023 - Welcome - An introduction to Nextflow
Chris Hakkaart shows how custom scripts, such as R or Perl o Python scripts, can be integrated into a Nextflow pipeline. nf-core/sarek (nf-core/bytesize #28)
Nextflow & nf-core Installation Made Easy! This week, Maxime Garcia (@gau) will present Running pipelines offline. This will cover: - Using nf-core tools to download a nf-core/bytesize: DSL2 coding style recommendations Part 1
nf-core/rnaseq (nf-core/bytesize #32) Join us to hear Phil Ewels ( chat with Maxime Garcia ( and Franziska Bonath Unable to start · Issue #1725 · nf-core/sarek
nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse. 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 week's bytesize, Cedric Notredame, Björn Lange, Francesca Bernini and Jose Espinosa-Carrasco are introducing the
sarek » nf-core nf-core/ampliseq (nf-core/bytesize #25)
This week, José Fernandez will present the nf-core/sarek pipeline in a very special episode of nf-core/bytesize talks focused on Nextflow community meeting in South Korea (2nd) 세션 내용 [실습] Nextflow 기초 트레이닝 (핸즈온 세션) [이론] Sarek 워크플로우
Nextflow Summit Boston 2023 - Eleanor Karp-Tatham '#8' written and performed by James Sarek Filmed by Roger Allen, Marcel Glover, Tamara Draycott, Gavin Radcliffe Special Chris Wyatt shows us how to use GitPod ( for testing, development, and training. Here are some of the links and
Live stream of Nextflow and nf-core training. Please post questions on Slack: 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 nf-core/bytesize: nf-core Subworkflows