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ncats / translator-workflows

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Workflow 5 Module 1 - Define a cohort #19

Open karafecho opened 5 years ago

karafecho commented 5 years ago

Module Overview

The intent of this module is to use Translator clinical knowledge sources (e.g., COHD, ICEES, Clinical Profiles) to define a patient cohort using any number of available feature variables (e.g., demographics, diagnoses, medications, clinical outcomes, laboratory measures). Note that data provenance must be retained, including inclusion criteria, exclusion criteria, sample size, statistics and P values, etc.

Comment This ticket is for general considerations about Workflow 5, Module 1 as a whole. Separate tickets may be created for issues specific to a particular submodule.

colinkcurtis commented 5 years ago

Using cwl-runner and the python 'iceesclient' I've been working on recently, I have a simple CWL wrapper which can now execute this operation.

colinkcurtis commented 5 years ago

First commit at:

https://github.com/ncats/translator-workflows/tree/master/Workflow5