Add reference database name to output of assign_taxonomy

[robinsleith]

The following section should be able to be modified to include the CFG$dada2_assignTaxonomy_nochim$refFasta in the filename, will be clunky with entire name (e.g. ASV_taxa_pr2_version_4.13.0_18S_dada2.fasta.csv) but that might be simplest solution for now.

ttaxa <- dplyr::as_tibble(taxa) %>% dplyr::mutate(ASV = names(fasta)) %>% dplyr::relocate(ASV, .before = 1) %>% readr::write_csv(file.path(CFG$output_path, "ASV_taxa.csv"))

[btupper]

Didn't we do this already? Or is this different? Argh - where are the example scripts? The can't be the ones that we currently show in this repos under Rscript/ can they?

[robinsleith]

No, I still havent figured out how/where to upload the "workflow" scripts

[robinsleith]

It looks like here might be the place? /mnt/storage/data/edna/dada/edna-dada2/Rscript

Then do the status, commit, push steps?

[btupper]

Let's get on the horn. I have from now until 230, and then again after 330-ish until close of business.

On Wed, May 5, 2021 at 1:50 PM Robin S. Sleith @.***> wrote:

It looks like here might be the place? /mnt/storage/data/edna/dada/edna-dada2/Rscript

Then do the status, commit, push steps?

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-- Ben Tupper (he/him) Bigelow Laboratory for Ocean Science East Boothbay, Maine http://www.bigelow.org/ https://eco.bigelow.org

[robinsleith]

https://smith.zoom.us/my/meetwithsleith

[robinsleith]

Wanna start now and pick up again later if we need?

[btupper]

Remind me what this is?

[robinsleith]

Instead of having it spit out ASV_taxa.csv have it return $refFasta_ASV_taxa.csv