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