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