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Old 11-11-2019, 07:10 AM   #1
Physalia-courses
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Location: Berlin

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Default Nextflow: Reproducible Containerised Scientific Workflows across Clusters and Cloud

Nextflow: Reproducible Containerised Scientific Workflows across Clusters and Cloud

https://www.physalia-courses.org/cou...hops/course60/

Nextflow is a widely adopted workflow system for running high-throughput, data-intensive applications across cloud and on-premise infrastructure.

It has fast become one of the primary technology platforms for computational workloads in life sciences.

The framework allows scientists to write code in any scripting language, define software dependencies with containers, connect tasks with the event-driven dataflow programming DSL and then deploy anywhere: local machines, grid computing systems or public cloud infrastructure.

Nextflow developers Paolo Di Tommaso and Evan Floden will present this popular two days training event.

The workshop is intended for users to become quickly proficient in Nextflow technology, starting from basic through to advanced concepts.

Intensive training is provided across 14 Nextflow topics with each topic designed to last between 45 to 60 min and includes talks, live demonstrations and practical sections which all participants can complete.

Day One

Overview of Nextflow workflow system
Nextflow language syntax and data structures
Dataflow variables and channel semantics
Nextflow operators and processes
Simple pipeline implementation
Modules and DSL2
Pipeline sharing & best practice for reproducibility

Day Two:

Nextflow configuration and profiles
Managing dependencies with containers
Executors & deployment scenarios
Error recovery & strategies for error handling
Workflow and runtime metadata and events
Common implementation patterns
Implementation of a variant calling pipeline

A repository will be provided with all the necessary material and software as well as an AWS cloud environment to carry out the activities in the relevant practical sessions.
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nextflow, pipeline automation, reproducibility, work flow

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