Found a bug in CLI, raw_fastq_path is relative to assembly working directory, not relative to wherever you ran ipyrad from, this was not the behavior i expected. Is this intentional? If so i can learn to live with it ;p
I don't think we need to chdir at any point, we should always be using abs paths.
I'm not going to have time to work on ipyrad much this week. Should I push the changes I have for step7 on a separate branch so you can get a gist for the direction I'm going with it, and hack on them too? Or just push to master and not worry about step7 being broken at this point?
agreed... I'm still working on fine tuning the preview mode pipeline for glenn's gbs data, if you don't have enough high depth clusters going in to step 4 it isn't happy, also trying to get more informative preview mode output.
Hm, why don't you push a branch, that's a good idea. I'll check it out.
This is probably obvious, but you can't have more than one assembly using the same working directory. Especially for any step that uses zcat_make_temps, because they will end up writing over the same tmpdir. Could fix this by prepending data.name to tmpdir, if you think this could be a problem.
Lol, i was exactly running to analyses simultaneously. I'll fix it.
In CLI the name does get grabbed from working_dir, it's working_dir.rsplit("/", 1). It works, but i'm not super happy with it, i'd be open to other ideas.
I wrote a routine to iterate over various values (between .5 and 4 million sequences) for preview_truncate and get timing information for each step. Side-effect is it collects information about whether any step failed, so we could maybe use it as a crude test skeleton.