Developing reproducible bioinformatics workflows with Nextflow

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Category
Courses
Date
2020-01-23 09:00 - 2020-01-24 17:00
Venue
University of Liège, GIGA institute, Leon Fredericq auditorium
Email
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Immunology
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Attachment
Developing reproducible bioinformatics workflows with Nextflow

Workshop limited to 30 participants
Cost: 210 Euros/pp
Venue: University of Liège, GIGA institute, Leon Fredericq auditorium
Trainers: Paolo Di Tommaso, Evan Flowden
Contact and inscription: Luc Cornet, This email address is being protected from spambots. You need JavaScript enabled to view it.

Program
Day One, basic concepts :
1. Overview of Nextflow workflow system
2. Nextflow language syntax and data structures
3. Dataflow variables and channel semantics
4. Nextflow operators and processes
5. Simple pipeline implementation
6. Modules and DSL2
7. Pipeline sharing and best practice for reproducibility


Day Two, advanced concepts :
1. Nextflow configuration and profiles
2. Managing dependencies with containers
3. Executors and deployment scenarios
4. Error recovery and strategies for error handling
5. Workflow and runtime metadata
6. Common implementation patterns
7. Implementation of a variant calling pipeline


Informations to participants
Prerequisites :
1. Unix laptop
2. First experience with bioinformatics pipelines

Participants should be able to create and run their pipelines with Nextflow after this workshop.