Retrieve sequencing metrics from cg instead of cgstats

Clinical-Genomics / clinical_EPPs

EPPs used in clinical genomics LIMS

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Retrieve sequencing metrics from cg instead of cgstats #238

Closed seallard closed 1 year ago

seallard commented 1 year ago

This PR removes the dependency on cgstats from lims, retrieving the necessary sequencing metrics from cg instead. Part of project https://github.com/Clinical-Genomics/project-planning/issues/482.

The new script does the following (except for setting the perfect index reads)

This version is a:

[ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

seallard commented 1 year ago

I can't access the stage environment ssh gls@clinical-lims-stage.scilifelab.se, I'll mark this as ready for review once I have access and have tested the script

Karl-Svard commented 1 year ago

I can help you with that when you feel ready. But before we start the testing I think it would be good to have a discussion on where to add this new script. The plan is to deprecate clinical_EPPs as soon as possible, so cg_lims is the prefered location to add new/modified EPPs to. It could also be good to have a quick crash course into the lims repos, regarding how the configs are set up etc.

seallard commented 1 year ago

This PR should opened in the https://github.com/Clinical-Genomics/cg_lims instead

seallard commented 1 year ago

I can help you with that when you feel ready. But before we start the testing I think it would be good to have a discussion on where to add this new script. The plan is to deprecate clinical_EPPs as soon as possible, so cg_lims is the prefered location to add new/modified EPPs to. It could also be good to have a quick crash course into the lims repos, regarding how the configs are set up etc.

Thanks!