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Building workflows with Pim #11
Building workflows with the Common Workflow Language.
There are several workflow tools for bioinformatics. Interoperability (the I in FAIR) is however often still a problem. In the context of creating a workflow that can easily migrate an open source workflow from Naturalis (see internship: https://www.rijkzwaancareers.com/careers/joint-internship-bioinformatics-rijk-zwaan-and-naturalis ) we're going to try out the CWL standard by creating a workflow with the Rabix Composer GUI and then running it locally with the CWL reference tool. Since CWL has multiple interpreters (toil, nextflow), it should afterwards be easier to run this workflow anywhere.
Check out the preparation guidelines below
Time and Place
Where: Room D1.113, Science Park 904
Prior knowledge required
A graphical interface will open
Step-by-step activities for the hour
Creating a test file, initialize our Rabix workspace and a first tool wrapper
Now try eSciencecenter's scriptcwl
Additional reading material
Thanks for adding me to the schedule, Marc! Just to give some context of a CWL project:
If anyone knows BSc or MSc students interested in this topic they can apply for a paid internship in on CWL-ing an open source workflow together with Naturalis! Contact me at email@example.com if there are questions! https://www.rijkzwaancareers.com/careers/joint-internship-bioinformatics-rijk-zwaan-and-naturalis