MDM: Exclude the failed Sequencing Run from the mart

[victorskl]

Context;

There are few legacy Sequencing Runs that are actually failed.

We have already cleaned up FASTQs (if any) from these failed Runs.

However. Legacy system meta records did not mark these Runs as failed yet.

Actions;

• Identify these Runs
• Exclude them out from data mart tables

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Side note: This activity forms part of the MDM (master data management) process.

[victorskl]

Exclude

230323_A01052_0146_BHN5HHDSX5

Traces:

• https://umccr.slack.com/archives/C05QUD8ETT7/p1757035916241479
• https://github.com/umccr/research-projects/issues/37#issuecomment-3252108187

select * from legacy.data_portal_sequence where instrument_run_id = '230323_A01052_0146_BHN5HHDSX5';
select * from legacy.data_portal_sequencerun where instrument_run_id = '230323_A01052_0146_BHN5HHDSX5';

• https://umccr.slack.com/archives/C8CG6K76W/p1679532162128789 (emergency stop requested)
• https://umccr.slack.com/archives/C8CG6K76W/p1679680766583509 (run succeeded at BSSH)
• https://umccr.slack.com/archives/C8CG6K76W/p1679680767842619 (emergency stop triggered)
• no further informatics processing for this Run
• replacement and superseded by Run 230324_A00130_0250_BHN3JVDSX5
  • https://umccr.slack.com/archives/C8CG6K76W/p1679618563477589

[victorskl]

Exclude

200619_A01052_0018_AH5LYGDSXY

Traces:

• https://umccr.slack.com/archives/C8CG6K76W/p1592962641060600 (FC issue and coverage is short)
• Run 18 is marked as Failed in legacy processing record sheet

select illumina_id, library_id, notes from psa.spreadsheet_google_lims where illumina_id = '200619_A01052_0018_AH5LYGDSXY';

• https://umccr.slack.com/archives/CP356DDCH/p1694485916229579 (Team has checked for depth coverage & consensus to purge the Run 18 FASTQ from the system record)

select * from legacy.data_portal_sequence where instrument_run_id = '200619_A01052_0018_AH5LYGDSXY';
select * from legacy.data_portal_sequencerun where instrument_run_id = '200619_A01052_0018_AH5LYGDSXY';

• replacement and superseded by Run 200624_A01052_0019_BH5L7WDSXY

[victorskl]

The https://github.com/umccr/research-projects/issues/50 is a part of this MDM process to building knowledge table and master records.