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BigelowLab / edna-dada2

Maine eDNA dada2
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Two assign_taxonomy calls in my version of dada.R #2

Closed robinsleith closed 3 years ago

robinsleith commented 3 years ago

My version of the dada.R script (from the weeds-workshop) has two assign_taxonomy calls, see below. It looks like the top version is not written, can this be removed?

taxa <- dadautils::assign_taxonomy(seqtab.nochim, 
                                   refFasta          = CFG$dada2_assignTaxonomy_nochim$refFasta, 
                                   taxLevels         = CFG$dada2_assignTaxonomy_nochim$taxLevels, 
                                   minBoot           = CFG$dada2_assignTaxonomy_nochim$minBoot, 
                                   outputBootstraps  = CFG$dada2_assignTaxonomy_nochim$outputBootstraps, 
                                   verbose           = CFG$dada2_assignTaxonomy_nochim$verbose, 
                                   multithread       = CFG$multithread,
                                   drop_levels       = "Species")

taxa <- dadautils::assign_taxonomy(seqtab.nochim, 
                                   refFasta          = CFG$dada2_assignTaxonomy_nochim$refFasta, 
                                   taxLevels         = CFG$dada2_assignTaxonomy_nochim$taxLevels, 
                                   minBoot           = CFG$dada2_assignTaxonomy_nochim$minBoot, 
                                   outputBootstraps  = CFG$dada2_assignTaxonomy_nochim$outputBootstraps, 
                                   verbose           = CFG$dada2_assignTaxonomy_nochim$verbose, 
                                   multithread       = CFG$multithread,
                                   drop_levels       = "Species",
                                   save_file         = TRUE,
                                   filename          = file.path(CFG$output_path, "taxa.csv"))
btupper commented 3 years ago

Yes