Use sambamba for duplicate marking. #1082
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We weren't using the barcode tag feature in these pipelines, but if we were we could bring back a picard version.
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I'll let John and others review, but I support this change as one that increases the speed through parallelization while using the same duplicate marking strategy and producing essentially identical results. |
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In porting the FDA metrics pipelines to the WDL workflows I ran into that those had been updated to switch duplicate markers but these had not. This carries that change over to the CWL version. I haven't tried running it on the immuno.cwl yet--thought I'd open this and see if it's something we wanted to do before running a test.