Incorporated Cutadapt for primer removal and binning #72
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…ts by primer, then trimming
…er Cutadapt-based splits
…ld have happened prior
…Still needs some cleanup but works.
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Merging now. @ChristosMatzoros heads-up these changes are coming; unfortunately the Cutadapt stats will take some wrangling to integrate to MultiQC, so take your time. Currently QIIME 2 only outputs Cutadapt stats as a text-based log file, so we'll have to do some text scraping -- but it's not a priority for now. If you're curious though, here's a toy example log: (These changes should've come in a fork but the branch I originally created for minor changes ballooned, whoops!) |
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Closes #51 and #62. Introduces Cutadapt to the workflow for both primer removal and binning. Though it may not be the most computationally efficient method, the workflow takes a single FASTQ input artifact and splits it into N artifacts depending on the N primers provided by the user.
As a result, this removes the former FASTQ split processes. I'm open to further discussion on whether we should bring that back for efficiency's sake.