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GGR-cwl User Guide

CWL workflows are decoupled and independent of the platform in which they are run. The CWL group provides detailed User Guides full of examples for each release of the standard (e. g. draft-3, v1.0) that should allow you to navigate the challenges of writing your own pipelines. But if you are new to CWL you might be missing some real life examples of how to use those documents. The reference implementation cwltool unfortunately does not include a wiki at the moment.

This wiki will walk you through the steps in order to run the pipelines used in the GGR project, using cwltool.

GGR Worflows are now written in v1.0 syntax

Our group was an early adopter of CWL even before the first official release of the standard (v1.0). Around that time, draft-3 was the latest edition, and that is why all the command line tools and workflows were originally written and can still be found in draft-3 syntax. The pipelines have now been translated and adapted to v1.0 syntax, and we don't plan to maintain and update the draft-3 versions.

Table of Contents

• 0. Required Software
• 1. Setting up the Environment
• 2. Using cwltool