am I correct: if I run the pipeline first with dada2 and gtdb and then later with qiime and a custom classifier with the same workdir and '-resume', the output in qiime2/abundance_tables will still be based on the dada2 output? and not on the qiime output? based on the docs, you cannot choose which taxclassifier supplied the data to the downstream qiime2 analysis? So I would have to rerun from scratch to skip dada2 tax all together

You can run the pipeline initially with dada2 and gtdb with

--outdir results_dada2gtdb

. Then run the pipeline again with

--outdir results_qiimecustom -resume

in the same directory. The pipeline will re-use what it can and re-do what it must. The two results directories will have some overlap because cached steps will still have their files copied to the results folder. But you will have reduced computing time and have both analysis separated. Is that answering your questions?

Exactly, thanks