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Clinical-Genomics / cg

Glue between Clinical Genomics apps
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Add store completed functionality to microsalt workflow #779

Closed barrystokman closed 3 years ago

barrystokman commented 3 years ago

Since cg version 13.3.0 it is possible to store a completed microSALT analysis in Housekeeper with the command cg workflow microsalt store analysis and providing it with a path to a deliverables file.

New CLI functionality needs to be added that will enable storing of all completed microSALT analyses using cg workflow microsalt store completed

Typically the deliverables file is stored under the run directory of the ticket, e.g. home/proj/production/microbial/results/ACC7093_2020.9.28_9.35.34 and is generated after the analysis.

Option: store all deliverables files in one folder.

Use https://github.com/Clinical-Genomics/cg/blob/30775ea7f7100d66a1d0cd02d24f80ddcc78c172/cg/store/api/status.py#L94 to get all microsalt analyses to be stored.

henrikstranneheim commented 3 years ago

@barrystokman Is this done?

barrystokman commented 3 years ago

@henrikstranneheim no, I actually need to implement a fix to get it to fully work, I'll put an item on the project board for it. It's about correcting the path to the deliverables file and the status of the analysis not being set in the run CLI command

barrystokman commented 3 years ago

WIP PR here: https://github.com/Clinical-Genomics/cg/pull/813

Mropat commented 3 years ago

All done now I think