Use of --isolate flag, and update of SPAdes assembler

[talnor]

Description

Summary of the changes made:

• Changed assembly command to exclude the --careful flag by default.
• Change assembly command to include the --isolate
• Updated spades assembler to 3.15.5

Fix for #164.

Primary function of PR

• Hotfix
• Patch
• 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

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Test routine to verify the stability of the PR:

• us
• install branch in stage
• cg workflow microsalt start vocalcoral

Test results

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

Sign-offs

• microSALT version is updated in microSALT/init.py
• Code tested by @octocat
• Approved to run at Clinical-Genomics by @sylvinite

[karlnyr]

This seems to set the default to --uncareful which is the behavior we want, neat!

[talnor]

Failed samples pass with updating settings. Typing of other samples remain the same.

v.3.3.6

v.3.4.0