Patching struct

[sylvinite]

Description

The features of this PR primarily concerns internals

Summary of the changes made:

• Added HK delivery file generation.
• Assemblies cropped at 1k nodes
• Stability upgrades to lower the chance of read-only lock

The HK delivery file means external programs can trend the results easier. No conflict with existing analysis exists.

Primary function of PR

• [ ] Hotfix
• [ ] Patch
• [X] Minor functionality improvement
• [ ] New type of analysis
• [ ] Backward-breaking functionality improvement
• [ ] This change requires internal documents to be updated
• [ ] This change requires another repository to be updated

Testing

Test routine to verify the stability of the PR:

• _bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh patching_struct_
• us
• _source activate S_microSALT_
• microSALT analyse project ACC5551

_Verify that the results for projects ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx Also review that the newly produced delivery file is present in the results folder, and is a valid json.

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Results for project ACC5551 are identical. Somehow the TravisCI test fails; but manual review of the logs review no errors (other than an insignificant warning about escaping characters). As such the TravisCI test has manually been considered to be passed.

Sign-offs

• [x] Code tested by @sylvinite
• [x] Approved to run at Clinical-Genomics by @sylvinite

[sylvinite]

Manual review of Travis/Branch shows that automatic tests resolve successfully.