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The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are joining together for a unified event to be held in Portland, Oregon, United States, June 25-30, 2018.  The event features two days of training, a two day meeting, and finish with two or four days of intense collaboration at the GCC OBF CollaborationFest Core and Encore events.  The meeting will feature joint and parallel sessions, and shared keynotes, poster and demo sessions, and social events.  Colocating GCC and BOSC will bring together the widest possible community of bioinformatics developers and practitioners into a single place.  At this event the whole will be greater than the sum of the parts.

The event is organized by Oregon Health & Science University and will be held at Reed College, a small liberal arts college in Portland. Conference housing is available in two Reed College residence hall complexesPortland is a vibrant city in the American Northwest, close to the Cascade Mountains, the Oregon Coast, and the Columbia River. 

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

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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-Essen | Department of Medical Oncology, Harvard Medical School | https://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
Training Venue 1