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Extract and capture LibraryRun yield and QC pass #447

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victorskl opened this issue Apr 21, 2022 · 2 comments
Open

Extract and capture LibraryRun yield and QC pass #447

victorskl opened this issue Apr 21, 2022 · 2 comments
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feature New feature orcabus triage & trello Triage and migrate into respective Trello project

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@victorskl
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victorskl commented Apr 21, 2022

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.

# 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:

Actions:

  • Implement it
@victorskl victorskl added the feature New feature label Apr 21, 2022
@victorskl victorskl added this to the Release 1.0.0 milestone Apr 26, 2022
@victorskl victorskl removed this from the Release 1.0.0 milestone May 2, 2022
@victorskl victorskl added the triage & trello Triage and migrate into respective Trello project label May 8, 2023
@victorskl
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More related sample that need QC go/no-go

umccr/RNAsum#109

@victorskl
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Labels
feature New feature orcabus triage & trello Triage and migrate into respective Trello project
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