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