Nathan Sheffield

it could work like this: ``` project_modifiers: filter: - attribute: protocol include: ["ATAC-seq"] exclude: ["RNA-seq"] ``` for each attribute, you have to have either an include, or an exclude, or...

is it just that pytests require the multi flag to be set? not sure this is a bug...

I think all the pypiper tests set `multi=True`. it's just what you have to do to use pypiper with pytests. look at all the existing pypiper tests. I think they're...

Another issue is that I can't figure out how to map the config options to configure pipestat the way I want it. I don't know what `pipestat_project_name` maps to, and...

Just another example where this bit me again. I wanted to pass `multi_pipeilnes=True` to pipestat, when I'm constructing my `pypiper.PipelineManager`, but this is not documented. The way to do it...

ok, then the docs are incorrect. pipestat is not the recommended way, it's the *only* way :)

yes, I agree with everything you state. I think basically nobody uses the logmuse to set the logfile path, so it hasn't been a problem. But you're right it could...

One hint is this message: ``` These results exist for 'DEFAULT_SAMPLE_NAME': Time These results exist for 'DEFAULT_SAMPLE_NAME': Success ``` It looks like there might be a bug somewhere with a...

I think `pipestat_sample_name` is not being passed through to pipestat

actually I think it's `pipestat_results_file` that's not working correclty...