Scattering CWL across Tabular Samples; and Interactive Computing Environments from CWL

Presenter: Nathan Sheffield (@nsheff), University of Virginia

Session 1 (Americas-EMEA) Monday, February 8th 15:15 UTC

Summary: “This talk introduces two projects that provide new capabilities relevant to CWL. First, we often encounter sample metadata as a CSV-formatted sample table, but I found no easy way to run a CWL workflow on each sample in such a table. To address this, I introduce looper, which scatters a CWL workflow on tabular data. Second, I have wanted to start an interactive terminal session using the same containerized computing environment that would run my workflow. This is useful to troubleshoot workflows, to explore data interactively, or to test different approaches. But it’s challenging because the container images are tightly coupled to the CWL workflow. To address this, I introduce Bulker, which simplifies interactive use of multi-container environments. It keeps commands identical to native commands, but runs them in containers behind the scenes. With bulker cwl2man, you can extract the images from a CWL workflow and create a standalone interactive environment.”

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