Extract and capture LibraryRun yield and QC pass

[victorskl]

Context:

• Pipeline has LibraryRun data model that track the sequenced-library i.e. as they are appeared in SampleSheet.csv of the Run directory.
• Hence, this LibraryRun won't track a library such as those that has failed at library kit prep stage at Lab side.
• Collection of LibraryRun for the said SequenceRun is guaranteed avail in Portal when BSSH SequenceRun reach to PendingAnalysis status. Then we start BCL Conversion.
• After BCL Conversion (and WGS Alignment QC), we wish to update a couple of fields on this LibraryRun data model. Current fields of interest are as follows.

data-portal-apis/data_portal/models/libraryrun.py

Lines 30 to 40 in a17678f

	# yield achieved with this run (to be compared against desired coverage defined in metadata)
	coverage_yield = models.CharField(max_length=255, null=True)
	# current overall QC status
	qc_pass = models.BooleanField(default=False, null=True)
	# could be progressive status from QC workflow pass to QC metric eval
	qc_status = models.CharField(max_length=255, null=True)
	# could be used for manual exclusion
	valid_for_analysis = models.BooleanField(default=True, null=True)

Use Case:

• This information can augment on automated Tumor/Normal Paring decision logic
• Example reproducible case: SBJ01954 - see https://umccr.slack.com/archives/C8CG6K76W/p1650332699060189

Actions:

• Implement it

[victorskl]

More related sample that need QC go/no-go

umccr/RNAsum#109

[victorskl]

QC feedback loop

https://umccr.slack.com/archives/CCC5J2NM6/p1718591802341509