This code copies .qmd files over to Terra. They don't appear in the Analyses tab like .Rmd and .ipynb file would, but they are present under Data/Files/notebooks. Since there are three options to copy over now I didn't know how you wanted to handle multiple combinations so I just went with 'ipynb', 'rmd', 'qmd', and 'all'. I did test this using my previously created test anvil workspace, as_workspace('~/AnVILBulkRNASeq', namespace = 'bioconductor-rpci-anvil', name = 'test-quarto', create = FALSE, update = TRUE, type = 'all', quarto = 'convert'). In order for this to work I created .qmd files for each of the vignettes, that way there were actual .qmd files to copy over.
This code copies .qmd files over to Terra. They don't appear in the Analyses tab like .Rmd and .ipynb file would, but they are present under Data/Files/notebooks. Since there are three options to copy over now I didn't know how you wanted to handle multiple combinations so I just went with 'ipynb', 'rmd', 'qmd', and 'all'. I did test this using my previously created test anvil workspace,
as_workspace('~/AnVILBulkRNASeq', namespace = 'bioconductor-rpci-anvil', name = 'test-quarto', create = FALSE, update = TRUE, type = 'all', quarto = 'convert'). In order for this to work I created .qmd files for each of the vignettes, that way there were actual .qmd files to copy over.