Fix `wgs_tumor_normal` alignment engineParameter override for many FASTQ input files

[victorskl]

Context:

Also known as "library 4 lanes split"

Case 1:

• Go to https://portal.umccr.org/subjects/SBJ00723/launch-pad/wgs-tn
• Observe amount of FASTQ files input

Case 2:

• Go to https://portal.umccr.org/subjects/SBJ00576/launch-pad/wgs-tn
• Observe amount of FASTQ files input

Team investigation:

See Slack thread by team on investigation:

• https://umccr.slack.com/archives/C8CG6K76W/p1716190793070379
• https://umccr.slack.com/archives/C025TLC7D/p1691624686247369?thread_ts=1691532027.452509&cid=C025TLC7D

Issue:

Upstream ICA WES engineParameter for TES; by default, the relevant flag set to auto as follows.

"tesUseInputManifest": "auto"

By changing engineParameter override to never should counter the issue.

"tesUseInputManifest": "never"

Action:

• Confirm setting the flag to "never" really solve the issue
• Improve the Portal operation QoS by fixing it

[victorskl]

How to add EngineParameter override to SecondaryAnalysisHelper in workflow.

Follow ctTSO scatter flag override

https://github.com/umccr/data-portal-apis/blob/7526347/data_processors/pipeline/domain/workflow.py#L243-L245

[victorskl]

Potential fix snippet:

        if self.type == WorkflowType.TUMOR_NORMAL:
            # <link to upstream issue pointer, if any>
            engine_params.update(tesUseInputManifest="never")

Need to run full test suite.

[victorskl]

In COLUMN_PI cohort, we leveraged this tesUseInputManifest = "never" flag.

https://github.com/search?q=repo%3Aumccr%2Fbiodaily%20tesUseInputManifest&type=code

---

Note though: This has done "Out-of-Band" [1] workflow run by directly launching at ICA WES. It involves couple of manual steps.

REF:

1. https://github.com/umccr/data-portal-apis/blob/dev/docs/pipeline/portal_run_id.md

[victorskl]

we can enable this for all workflow types.

ditto #693 convo