Is there a way to get the visualizations workflow to only access and compare data for a subset of the samples that were run through the biobakery workflows pipeline? I see the custom metadata.tsv allows for exclusion of features, but I don’t see an option for exclusion of samples. If I remove reference to those samples in the metadata.tsv, an error tells me that there’s data that’s not accounted for instead of ignoring that data.
I figured a workaround could be to create a new directory and only move the biobakery_workflow data analysis output into it for the samples I wanted to look at and use that with the slimmed down metadata.tsv, but I assume that also means I need to regenerate the merged files from the data analysis (counts, etc.,.) that were previously made using the full data set. As a result, I tried to re-run the data analysis workflow on a directory that already had the main output files for the samples I wanted, thinking it would skip trying to remake those files once they were detected and jump straight to only making the merged and count files, but instead it tried to start generating the output all over again (instead of printing out skipped repeatedly for those generation steps). Not sure if this would have been a viable workaround anyways, but I’m not sure why those files weren’t detected and any assistance with understanding what it’s looking for that wasn’t detected to allow for this would also be appreciated.