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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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Next release: 2019-03-23 #123

Closed HenrikBengtsson closed 5 years ago

HenrikBengtsson commented 5 years ago

Hi @ivan108, sorry for the radio silence - I've seen you done a lot of great work on the pipeline since the latest release. Thxs.

Do you think it's a good time to try to do another freeze and release a new version? ...which involves running all real-world tests etc., so we need to synchronize/freeze.

Either way, would you mind adding entries on what you've done to NEWS.md? That would also help me catch up.

ivan108 commented 5 years ago

Yes, you are right, I am lagging behind on updating NEWS, will do... And as soon as I get new Pindel working, we can run tests and release new version.. Thx!

HenrikBengtsson commented 5 years ago

So, you don't think the new Pindel (Issue #122) will break backward compatibility? If it's major work/change, I'd say it could be saved for the following release.

ivan108 commented 5 years ago

Just to be on a safe side, I want to check compatibility of the output of new pindel. If it is identical, we can include it in the new release, otherwise move to the next..

HenrikBengtsson commented 5 years ago

Given your latest findings/issues with using a new/newer Pindel version, I'd say we should hold back on that one for a later release to minimize the number of possible surprises. Safer to many small releases and few large ones.

ivan108 commented 5 years ago

I added some most significant changes to NEWS.md, feel free to edit.

It looks like the new pindel have some differences in the VCF output which breaks our custom post-processing scripts. So, it needs some work, but we can go ahead with testing and releasing current version as is...

HenrikBengtsson commented 5 years ago

Ok, I've just started the testing based on devel commit 07a014c.

HenrikBengtsson commented 5 years ago

LG3_Pipeline 2019-03-23 is now released and available on TIPCC:

$ module load CBC lg3
$ lg3 --version
2019-03-23 (commit 749df93)