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hammerlab / ngsdiagnostics

Diagnostic Scripts for an NGS Pipeline
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Step-specific parsing of GATK command content #13

Open hammer opened 10 years ago

hammer commented 10 years ago

There's important information in each step, including input and output files, that we're not currently capturing.

hammer commented 10 years ago

I added some code for parsing command-line arguments to GATK tool invocations at https://github.com/hammerlab/ngsdiagnostics/commit/5e91dee836c5bfd4da3854f980000a2002ca70ac. I'm not quite sure how best to bring this data into the database.

hammer commented 10 years ago

I took a first cut at bringing this data into the database in https://github.com/hammerlab/ngsdiagnostics/commit/2bf8944fbd2822e61373b6304e6b68623f9e6821. I'm going to revisit the schema we're using to better accommodate this information before closing out this issue.