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UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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make check errors on develop_c4 branch #152

Open HenrikBengtsson opened 2 years ago

HenrikBengtsson commented 2 years ago

@ivan108, I've enabled make check checks on the develop_c4 branch too (was only develop before).

It signals several potential issues (https://github.com/UCSF-Costello-Lab/LG3_Pipeline/actions/runs/1296944217) that should be fixed.

ivan108 commented 2 years ago

Can't figure out the problem with check_demo, it complains about assert_pwd . Error SC2119: Use assert_pwd "$@" if function's $1 should mean script's $1.

Shell we just disable that?

Other checks pass OK..

HenrikBengtsson commented 2 years ago

Thanks. I'll have a look later to see what's up. Could be a false positive.

HenrikBengtsson commented 2 years ago

Please push what you've got this far.

ivan108 commented 2 years ago

Pushed all. Let me know if you edit anything, so that I remember to pull..

ivan108 commented 2 years ago

One more thing, I couldn't handle the SC2012 issue in lg3-status, so I just disabled it. The actual code looks like that: MESS=$(ls -sh "${OUT}" | cut -d' ' -f1) The idea is to extract file size in human format.

HenrikBengtsson commented 2 years ago

One more thing, I couldn't handle the SC2012 issue in lg3-status, so I just disabled it.

Oh, now I see:

https://github.com/UCSF-Costello-Lab/LG3_Pipeline/commit/faf915e84e23bc008d1a6f64f44290999ee5b206

I see you've also disabled SC1091. Please don't do that. I've undone them. If it's that you don't know how avoid SC1091:s when checking locally, let me know, and I'll try to come up with some instructions.

HenrikBengtsson commented 2 years ago

Ivan, I'm going through the commit history and I see you've disabled loooooots of these checks. They are there to help us avoid bugs. We need undo all of the ones you've disabled and start over from scratch. Can you please undo all of them? I started doing it but then I realized there are lots of edits to do.