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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 are two days of training, a two day meeting, and two to four days of intense collaboration.  The meeting will feature joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC brings together the widest possible community of bioinformatics developers and practitioners into a single event.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

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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.
Snakemake
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.
Nextflow
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
Prerequisites
  • Linux command line experience

Speakers
JK

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