Adding qza file for downstream analysis in R

[asgarhussain]

Description of feature

Is it possible to retain all the intermediate files in qza/qzv format so that it can be used directly in various downstream analysis using R.

[d4straub]

Hi there,
currently only a few qza are exported to the results folder, for example in
qiime2/input/
qiime2/representative_sequences/
qiime2/abundance_tables/
qiime2/phylogenetic_tree/
It is possible to increase that number by supplying a config with -c that contains essentially overwrites the publishDir block for the QIIME2 processes in conf/modules.config to also export qza/qzv files.
But to import tables in R, the usual tsv/csv/txt files that are already in the results folder should suffice.
Could you describe your usecase?

[asgarhussain]

Thanks for the quick response. I am using qiime2R package and ggplot2 for plotting distance matrix.

[d4straub]

I added the param --save_intermediates in the dev branch that will populate the results folder with all qza and qzv that I could find. Will be in next release.