[User Story] Add MSI analysis

[khurrammaqbool]

Need

MSI analysis was requested to be included to the workflow in #972

Suggested approach

Add MSIsensor-pro. See https://github.com/xjtu-omics/msisensor-pro/wiki and Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, et al. MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability. Genomics Proteomics Bioinformatics 2020,18(1). PDF for more details.

Considered alternatives

No response

Deviation

No response

System requirements assessed

• Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Risk assessment needed

• Needed
• Not needed

Risk assessment

No response

SOUPs

No response

Can be closed when

No response

Blockers

No response

Anything else?

No response

[ivadym]

Can you make sure the System Requirements section is filled out and the Can be closed when section has all the relevant issues and PRs linked? If anything's missing, please open new issues

[khurrammaqbool]

Store MSI score file in housekeeper to be able to fetch the scores from across the cases and analyse.

• Add housekeeper tag in the params of the rule
• Add a rule to the delivery rules
• Open an issue for the analysis to compute threshold when we at least 100 cases tumor-normal are analysed using BALSAMIC v16
• Add to Hermes Update files and tags for balsamic release 16.0.0 hermes#117

[khurrammaqbool]

Cases	DRAGEN TN MSI	BALSAMICv16 TN MSI
MSI1	80.359
MSI2	47.88
MSI3	60.979
MSI4	20.129
MSI5	48.28
MSI6	78.03
MSI7	81.579
MSI8	87.26
MSI9	70.68