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MMARINeDNA / metabarcoding_QAQC_pipeline

Pipeline scripts for initial quality control, ASV assignment, taxonomic classification, and preliminary data visualization
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Various Issues in `dada2QAQC.R` #23

Closed invertdna closed 11 months ago

invertdna commented 1 year ago

fastq_location argument passed from the wrapper script maybe should not have a trailing slash, because it creates a double slash in various paths and wrecks things.

Same thing happens with output_location argument, used at lines 178-181 here; creates double slashes and fails to write out

It seems like the difference between paste0() and file.path() is what’s creating these double-slash issues. You’ve got to pick one or the other and go with it.

Lines 144 and 146 can’t have the [[1]] in them, or else they throw errors? Maybe should be just errF <- dadaFs.lrn$err_out and errF <- dadaFs.lrn$err_out

invertdna commented 1 year ago

Correction on lines 144/146: sometimes it needs the [[1]], and I don't know when/why

alexandriai168 commented 1 year ago

In regards to the errF <- dadaFs.lrn$err_out[[1]] , this only throws an error when you only have 1 fastq file passed to the script/ only 1 makes it through the filtering step.

alexandriai168 commented 11 months ago

fixed trailing slashes- ran through the script and made sure all paths have only 1 "/" and updated the metabarcoding wrapper to reflect that! updated code pushed