common-workflow-language/hive-cwl-examples

Name: hive-cwl-examples

Owner: Common Workflow Language

Description: null

Created: 2016-12-19 12:50:29.0

Updated: 2017-12-04 20:41:52.0

Pushed: 2017-02-15 16:28:22.0

Homepage: null

Size: 16

Language: null

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README

Manual translation of https://hive.biochemistry.gwu.edu/cgi-bin/prd/htscsrs//servlet.cgi?pageid=bcoexample_1 into CWL

Notes: Not tested due to lack of source code

Things not translated, but could be added without breaking CWL compatibility

• usability_domain, could go in documentation or as a HIVE/biocompute specific extension
• xref
• keywords
• publication_status
• modification_date, creation_date
• “verification”
• that this is a subtype of the “antiviral_resistance_detection[ICD:B17]“, could have been done via a Workflow that contains the other Workflow and sets different defaults.

Questions about biocompute: what's the relationship between “pipeline” and the “type” field in the biocompute object?

How does BioCompute model the flow of data between steps? (Or is that implicit in the “script”: “obj.123123”?)

What is the priority for defaults amongst the antiviral_resistance_detection typedef, the biocompute object itself, and the referenced pipeline?

What is the meaning of the verfication_kit?