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