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"Building robust data processing pipelines with Python and Shell Scripts" by Sean La #179

scientificbruno opened this Issue Oct 17, 2017 · 0 comments


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scientificbruno commented Oct 17, 2017


Practical scientific computing involves extensive manipulation and processing of data. A pipeline is a self-contained program that performs a series of data processing steps with very little effort needed from the user. An ideal scientific computing pipeline is one that requires the user to only provide input data files and performs the rest of the computation on its own. Building pipelines like these are ideal for scientific research because they allow others to easily replicate computational research. In this workshop, participants will learn the basics of creating robust data processing pipelines using shell scripts and Python. Participants will build their own genetic variant caller pipeline to showcase this skill.

See below for required preparation.

Time and Place

Where: Room 7010, Library Research Commons, SFU Burnaby Campus

When: Thursday, February 1st, 2018 at 3:30 PM



Required Preparation

Assumed Knowledge

Basic shell scripting. Basic Python programming. Basic terminal usage.

Software Dependencies


Lessons Notes: TBA

Etherpad: TBA

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