wheaton5
Keep error logs
souporcell_pipeline.py captures STDERR streams to .err files but then deletes many of these, making troubleshooting difficult.
This PR simply deletes the lines that delete the .err files.
Sorry. I thought I was doing this on my own fork for the project. It is probably a good idea to keep these error logs for when things go wrong. I'll test it in my own fork and get back to you
No problem. Thanks. Let me know. I guess i was deleting them bc things were getting pretty crowded. Maybe they should be hidden files or maybe all stored in a subdirectory?
Never realised that I needed them until quite recently! But I do like the idea of keeping all log files in a separate directory. If the pipeline runs successfully to completion, then we can just delete them. But the pipeline has a habit of powering on even when things go badly wrong, and atm it can be quite hard to figure out where things start going off the rails. That's where these logs might come in handy. I've blown my quota on our HPC, so it might take a while to test this properly but I will let you know what I find!
Sounds good. This seems like the best path forward. Sorry to take up ur time.