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tgen / tempe

A container focused and streamlined iteration of the Phoenix pipeline
GNU General Public License v3.0
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Cleaned up stats2lims blocks and support for runbuilder level stat uploads #63

Closed bryce-turner closed 10 months ago

bryce-turner commented 10 months ago

Two main changes here, first is just some whitespace adjustments that the IDE was complaining about (with associated PEP codes)

The feature addition is that we now loop through the READGROUP level stats and upload these to the associated location in runbuilder. This has been tested on PCR-free markdup stats, which generates rgid level (e.g. lane level) duplicate metrics. This handles #55 though it requires PCR-free data, unless we were to reconfigure our markdup workflow to always use read group aware duplicate marking.

bryce-turner commented 10 months ago

Added @PedalheadPHX post merge for visibility, let me know if we'd like to revert these changes or make adjustments.