Decon (pronounced like “deacon”, rhymes with weaken) is a WDL workflow for decontaminating and concatenating paired Illumina FASTQs. It is designed for Mycobacterium tuberculosis complex and specifically the myco pipeline, but you could hack this for other pathogens if you’d like.

Decon imports almost all of its code from clockwork-wdl. If you are having issues that you think are related to the WDL, plea

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