Code

feature(dev-branch-pacbio)#3453

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diitaz93 merged 76 commits intomasterClinical-Genomics/cg:masterfrom dev-pacbio-flowClinical-Genomics/cg:dev-pacbio-flowCopy head branch name to clipboardAug 15, 2024

+2,234-647

Commits

Commits on Jul 22, 2024

• first draft

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Commits on Jul 23, 2024

• Merge branch 'master' into dev-pacbio-flow

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• add new classes

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• flesh out skeleton

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• iniital pacbio setup

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• Merge branch 'master' into dev-pacbio-flow

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• Apply suggestions from code review

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Commits on Jul 24, 2024

• Merge branch 'master' into dev-pacbio-flow

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• add pacbio run data generator (#3458)

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• Merge branch 'master' into dev-pacbio-flow

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• add PacBioRunFileManager (#3460)

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Commits on Jul 25, 2024

• Move the modules to the correct location (#3462)

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Commits on Jul 26, 2024

• refactor pacbio metrics parser (#3467)

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• PacBio - implement parsing of failed reads metrics (#3469)

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• setup dtos (#3472)

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• add(hk service to pacbio flow) (#3466)

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Commits on Jul 29, 2024

• add sample dto (#3475)

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• Merge branch 'master' into dev-pacbio-flow

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• small change in dto

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• add sample id to dto

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  b9c23ea

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• fix types of pacbio dto attributes

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• remove unused import

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• black

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• Add PacBio Data Transfer service (#3477)(patch)

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• abstract classes cleanup

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• fix self

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• add(pacbio store service) (#3478)

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• Merge branch 'master' into dev-pacbio-flow

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• add abstract method decorator and removed unused imports

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• add PacBio post processing service (#3481)

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• remove unused function in HK service

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Commits on Jul 30, 2024

• Add cli post processing (#3485)

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Commits on Jul 31, 2024

• Remove pbi file from post processing (#3491)

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• rename test module

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• add error handlers pacbio flow (#3487)

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• add dry run functionality to PacBio post-processing (#3483)

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• black

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Commits on Aug 7, 2024

• Merge branch 'master' into dev-pacbio-flow

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• Merge branch 'master' into dev-pacbio-flow

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• black

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• Merge branch 'master' into dev-pacbio-flow

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Commits on Aug 8, 2024

• Set PacBio sequencing times (#3518)

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• Merge branch 'master' into dev-pacbio-flow

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• Merge branch 'master' into dev-pacbio-flow

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Commits on Aug 9, 2024

• add CLI command to CLI

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• improve help docstrings

  diitaz93

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  b0501e7

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• add logging to post-process base

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  2606b19

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• Improve error raising with wrong run name

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  079d9c7

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• validate existence of run path

  diitaz93

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  53167d9

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• fix bug in PacBio service definition

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Commits on Aug 12, 2024

• Merge branch 'master' into dev-pacbio-flow

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Commits on Aug 14, 2024

• Merge branch 'master' into dev-pacbio-flow

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  b04330e

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• fix error handling logging

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  abccba0

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• rename dir (#3562)

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• Merge branch 'master' into dev-pacbio-flow

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• Merge branch 'master' into dev-pacbio-flow

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• reordered dto, metric and model attributes

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• add missing parameter to sample DTO

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• Merge branch 'master' into dev-pacbio-flow

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• fix names in model

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• Merge branch 'master' into dev-pacbio-flow

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• switch pacbio model column names back

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• apply column name change in crud

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• change dry run logging from debug to info

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• fix sample run metrics table name

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• Improve docsrings

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Commits on Aug 15, 2024

• Merge branch 'master' into dev-pacbio-flow

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• Make hifi_mean_read_length int

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• Make failed_mean_read_length int

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• Make polymerase reads int

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• Make sample metrics int

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• Make control metrics int

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• Add cell tag to bam file

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• Add cell tag to bam file and fix tag concatenation (#3571)

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• Merge branch 'master' into dev-pacbio-flow

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• Merge remote-tracking branch 'origin/dev-pacbio-flow' into dev-pacbio-flow

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