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nhoffman / dada2-nf

A Nextflow pipeline for processing 16S rRNA sequences using dada2
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WIP: Handle null seqtab in get_chim_dropped.R #51

Closed dhoogest closed 2 years ago

dhoogest commented 2 years ago

@nhoffman @mwohl Steve wanted a uniNGS experiment run which has a bunch of non-template controls in checkerboard arrangement to isolate amplifications. The low weight samples in the batch pointed out an omission in the newly added get_chim_dropped.R, in that in the event that no sequences survive filtering (dada.rds seqtab is NULL) the script errors out. I've added a conditional here to write a headers-only file in the empty scenario and am testing a bit more to see if there are downstream implications.

dhoogest commented 2 years ago

I'm gonna go ahead and merge this in. Tests passed