GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

Back To Schedule
Tuesday, June 26 • 3:30pm - 6:00pm
Command line workflow management systems: Snakemake and Nextflow

Sign up or log in to save this to your schedule, view media, leave feedback and see who's attending!

Snakemake Tutorial

Key:  -  | XB | IP | TD |  -  | CL

This session introduces command line and text based workflow management systems by the examples of Snakemake and Nextflow. We will start with an overview of concepts and challenges then spend an hour on each of these platforms.
We will show how to define a workflow in the Snakemake workflow language, and how to execute it using the Snakemake command line interface. In particular, we will show how Snakemake enables reproducible science by allowing
  • automation of every step of a data analysis from raw data to final figures
  • scalability of the workflow to any major computing architecture (compute server, cluster, grid, cloud) without having to modify the workflow definition
  • portability of the workflow by integration with the Conda package manager and Singularity containers.
This session will introduce the Nextflow framework, the tool basic concepts and how it enables the definition and the deployment of large-scale distributed computational pipeline in a portable and reproducible manner across cloud and clusters. In particular it will be discussed:
  • installation and introduction to the dataflow processing model
  • workflows parallelisation and scalability
  • portable workflows containerisation with Docker, Singularity and Shifter
  • cloud deployment strategies
  • Linux command line experience


Johannes Köster

Genome Informatics, Institute of Human Genetics, University of Duisburg-EssenDepartment of Medical Oncology, Harvard Medical Schoolhttps://koesterlab.github.io
avatar for Paolo Di Tommaso

Paolo Di Tommaso

Research Software engineer, Center for Genomic Regulation (CRG)

Tuesday June 26, 2018 3:30pm - 6:00pm PDT
Vollum Lounge Vollum College Center, Reed Campus