cg 80.1.0__py3-none-any.whl → 83.14.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cg/__init__.py +1 -1
- cg/apps/housekeeper/hk.py +1 -1
- cg/apps/tb/api.py +1 -1
- cg/cli/upload/mutacc.py +16 -3
- cg/cli/upload/scout.py +2 -2
- cg/cli/upload/utils.py +10 -1
- cg/cli/workflow/balsamic/base.py +29 -4
- cg/cli/workflow/microsalt/base.py +3 -1
- cg/cli/workflow/nallo/base.py +18 -38
- cg/cli/workflow/nf_analysis.py +2 -203
- cg/cli/workflow/raredisease/base.py +33 -51
- cg/cli/workflow/rnafusion/base.py +28 -3
- cg/cli/workflow/taxprofiler/base.py +21 -13
- cg/cli/workflow/tomte/base.py +17 -19
- cg/constants/constants.py +3 -3
- cg/constants/devices.py +6 -1
- cg/constants/gene_panel.py +3 -1
- cg/constants/lims.py +4 -0
- cg/constants/orderforms.py +1 -1
- cg/constants/pacbio.py +1 -0
- cg/constants/scout.py +6 -4
- cg/exc.py +12 -4
- cg/meta/compress/compress.py +7 -2
- cg/meta/delivery_report/nallo.py +1 -1
- cg/meta/delivery_report/templates/macros/ticket_system.html +1 -1
- cg/meta/observations/balsamic_observations_api.py +1 -1
- cg/meta/observations/mip_dna_observations_api.py +1 -1
- cg/meta/observations/nallo_observations_api.py +1 -1
- cg/meta/observations/observations_api.py +1 -1
- cg/meta/observations/raredisease_observations_api.py +1 -1
- cg/meta/tar/tar.py +5 -2
- cg/meta/upload/coverage.py +5 -5
- cg/meta/upload/raredisease/raredisease.py +3 -0
- cg/meta/upload/scout/nallo_config_builder.py +14 -0
- cg/meta/workflow/nallo.py +22 -95
- cg/meta/workflow/nf_analysis.py +11 -262
- cg/meta/workflow/raredisease.py +3 -112
- cg/meta/workflow/rnafusion.py +2 -34
- cg/meta/workflow/taxprofiler.py +2 -38
- cg/meta/workflow/tomte.py +2 -42
- cg/models/deliverables/metric_deliverables.py +1 -1
- cg/models/nallo/nallo.py +14 -64
- cg/models/nf_analysis.py +1 -41
- cg/models/raredisease/raredisease.py +0 -62
- cg/models/rnafusion/rnafusion.py +0 -26
- cg/models/scout/scout_load_config.py +1 -0
- cg/models/taxprofiler/taxprofiler.py +0 -42
- cg/models/tomte/tomte.py +0 -69
- cg/resources/nallo_bundle_filenames.yaml +282 -22
- cg/resources/raredisease_bundle_filenames.yaml +11 -1
- cg/resources/taxprofiler_bundle_filenames.yaml +20 -0
- cg/server/admin.py +51 -24
- cg/server/app.py +15 -4
- cg/server/endpoints/sequencing_run/dtos.py +21 -3
- cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py +29 -10
- cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py +20 -0
- cg/services/analysis_starter/configurator/configurator.py +1 -1
- cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/models.py +40 -1
- cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/nallo.py +3 -1
- cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/tomte_params_file_creator.py +3 -1
- cg/services/analysis_starter/factories/configurator_factory.py +4 -4
- cg/services/analysis_starter/tracker/implementations/balsamic.py +4 -1
- cg/services/analysis_starter/tracker/implementations/microsalt.py +4 -4
- cg/services/analysis_starter/tracker/implementations/mip_dna.py +4 -1
- cg/services/analysis_starter/tracker/implementations/nextflow_tracker.py +6 -4
- cg/services/analysis_starter/tracker/tracker.py +10 -6
- cg/services/illumina/backup/backup_service.py +29 -7
- cg/services/orders/validation/constants.py +3 -0
- cg/services/orders/validation/index_sequences.py +558 -0
- cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py +39 -18
- cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py +8 -2
- cg/services/run_devices/pacbio/data_transfer_service/dto.py +9 -3
- cg/services/run_devices/pacbio/data_transfer_service/utils.py +14 -7
- cg/services/run_devices/pacbio/metrics_parser/models.py +1 -0
- cg/services/run_devices/pacbio/sequencing_runs_service.py +35 -7
- cg/services/sequencing_qc_service/quality_checks/checks.py +18 -16
- cg/services/sequencing_qc_service/quality_checks/utils.py +82 -18
- cg/services/sequencing_qc_service/sequencing_qc_service.py +12 -10
- cg/store/crud/create.py +73 -42
- cg/store/crud/read.py +50 -2
- cg/store/crud/update.py +14 -3
- cg/store/models.py +88 -31
- cg/store/store.py +8 -1
- {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/METADATA +1 -1
- {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/RECORD +91 -90
- /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{nallo.py → nallo_sample_sheet_creator.py} +0 -0
- /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{raredisease.py → raredisease_sample_sheet_creator.py} +0 -0
- /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{rnafusion.py → rnafusion_sample_sheet_creator.py} +0 -0
- /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{taxprofiler.py → taxprofiler_sample_sheet_creator.py} +0 -0
- {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/WHEEL +0 -0
- {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/entry_points.txt +0 -0
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cg/__init__.py,sha256=RgHAoKbllDMi7ckyAB45aoTMtNGv5zZDVucQHnz9MkM,41
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cg/apps/__init__.py,sha256=pYf0vxo4iYQqURzFRYzqpOCdV8Cm9MWx0GHvJOz0EMg,315
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cg/apps/coverage/__init__.py,sha256=dJtsmNf8tODE2-VEomMIoYA7ugLYZAk_upsfOQCZeF8,27
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cg/apps/housekeeper/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/apps/housekeeper/hk.py,sha256=
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cg/apps/housekeeper/hk.py,sha256=J8ZERed6J5mzbNHikCqo2hH6gnc4MYCdJHjUJZJQlEs,28642
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cg/apps/invoice/__init__.py,sha256=1YWal0E1HPO5sdLOj9_JUwL_17Z2DSj7iJV5kEd8Q-4,32
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cg/apps/invoice/render.py,sha256=2U93Sdak_8v0j56qZLdcvBeofWO0ppiUqKNAaaCLCsU,4970
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cg/apps/tb/dto/create_job_request.py,sha256=ZTL491KYxBQu_nXxcl6hpuSsbM9mufjmWtE62_0RAL8,152
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cg/apps/tb/dto/summary_response.py,sha256=jwE1Pz0WAuKrytYdKX_VNLA_THEuKLr_JLb3CDwJA0g,929
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cg/cli/upload/genotype.py,sha256=Eu3IVrYSlM8rmwEXHiDD5Ai6fBjGQliBeg4vSFt5AFk,1488
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cg/cli/upload/gens.py,sha256=gUki1iCS3swqTaZChRNLKoFNw2dIeCnMxfBXiAQS6Ow,1929
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cg/cli/upload/gisaid.py,sha256=AS-dsBYH8ECPiop77MXUqosVqtUD1LpnFAr0BnybChM,598
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cg/cli/upload/nipt/__init__.py,sha256=r1bbsGXlNU2acSs7A-g6cyLtYkVS_NqT-Q_Lx52EbqA,23
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cg/services/analysis_starter/tracker/implementations/balsamic.py,sha256=f8JiVd4q83tsdSvdxvvaSV5y0-uPdey_7LL2Fyw4MSU,818
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cg/services/analysis_starter/tracker/implementations/microsalt.py,sha256=n5loG5ksQf54Kms0LPqRCTBwbksgtA7q51coWeQE014,1988
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cg/services/analysis_starter/tracker/implementations/mip_dna.py,sha256=_LBb4OhMbvB_vYvg7VQKwJ4MKeOvFjxFREw0z01zIVg,1009
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cg/services/analysis_starter/tracker/implementations/nextflow_tracker.py,sha256=BHvmgfhpFPh5fgytGBJv78Bp5ZH1z33ivoHwALChh_k,656
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cg/services/analysis_starter/tracker/tracker.py,sha256=_GsyH0AGY-9_uG9y9qpD7h58AsDIeauFzwe8dD9Xv9M,6346
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cg/services/decompression_service/decompressor.py,sha256=Sgb1oLaFxQjYjqCnsn8oJsf_rViv2_Xx1IjVP1-9AHs,973
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cg/services/deliver_files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/deliver_files/constants.py,sha256=SPBc_tz9c6OKqlzwwSNG-rN3ZIUc36N2vs4gMaMbbvI,635
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@@ -642,7 +643,7 @@ cg/services/fastq_concatenation_service/fastq_concatenation_service.py,sha256=3C
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cg/services/fastq_concatenation_service/utils.py,sha256=f2RY1lFnOPsgNX64Vew4Q9bXpfgKG_cb09eE3hgiCJg,3532
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cg/services/illumina/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/illumina/backup/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/illumina/backup/backup_service.py,sha256=
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cg/services/illumina/backup/backup_service.py,sha256=B5RBD9J2vqrWdieHpGnvvaer32-v_3Y5rAlCmA9m_0Y,16009
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cg/services/illumina/backup/encrypt_service.py,sha256=HCyxmBmoUjD6-9W04Esi4VLDrAge8LWjNZ6r-pQ3xOo,8714
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cg/services/illumina/backup/models.py,sha256=siFCpQn9S_uY7YK0kY0sZefUHd6dUZYYWTGNp8QOog4,670
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cg/services/illumina/backup/utils.py,sha256=I6Jr2AV2eWOXbqduvcGtVLrcZU9FtoyNldcp5lXzdow,4123
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@@ -694,14 +695,14 @@ cg/services/orders/storing/service_registry.py,sha256=ySnkLBqp1bM7I0ICWI_IkhjVgs
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cg/services/orders/submitter/service.py,sha256=Jn_ToVCPL5Y2PmtF281Usces4-f0ebMKPg6mTrronjQ,1953
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cg/services/orders/submitter/ticket_handler.py,sha256=PFW7v8CkSwCvfVG6zr2co8tv8C3XrkbDNwKcfqkOAnU,10261
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cg/services/orders/validation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/orders/validation/constants.py,sha256=
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cg/services/orders/validation/constants.py,sha256=fj7Jy4VAQ_AYdtaBKRGu7-xrorQ5bsQATbfLmY2db_E,1575
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cg/services/orders/validation/errors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/orders/validation/errors/case_errors.py,sha256=LpsErPsmxt3w4sUZfWIY_-Z6IxXVh70V1YCthTyPx4o,2314
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cg/services/orders/validation/errors/case_sample_errors.py,sha256=rBUIwelf8Z4O0_ztk98j6V1HqmDisL8DYkPPzSOZfKA,5698
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cg/services/orders/validation/errors/order_errors.py,sha256=hDqwv86IcmanxUCHLW1ExKg8Q4pGY-IaP6Bv76zJW4s,515
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cg/services/orders/validation/errors/sample_errors.py,sha256=OWi2iu8CHa-mAf9sWieEat9fh4rZd4eGn1GtLofKjJQ,4562
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cg/services/orders/validation/errors/validation_errors.py,sha256=8UPET3lrA0yLCFTvuqQ-fEMidq1iLxq7Sk3dUSTyt6M,1721
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cg/services/orders/validation/index_sequences.py,sha256=
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cg/services/orders/validation/index_sequences.py,sha256=m7ZQJICnvBtV-USBR8OFzKfgzeW-nQbeNlrTqL4lYvM,112601
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cg/services/orders/validation/model_validator/model_validator.py,sha256=S8SQqt-AHKQC6UL1HjjJaGWx48Ld-otpegnMq7NZOkc,704
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cg/services/orders/validation/model_validator/utils.py,sha256=yzNbWwsW_sNcS8zcQ2ugi3rRSgDONU-Zg4LZEKYsQ2s,6874
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cg/services/orders/validation/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -825,16 +826,16 @@ cg/services/run_devices/constants.py,sha256=-zI33OxI9XvXlyeSGw8jdqeuD_S1CFQRwWW5
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cg/services/run_devices/error_handler.py,sha256=BXVXy-8i4hr5jd7H5LEPs_sT7YzCzQMNoFV8m7y9BEc,636
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cg/services/run_devices/exc.py,sha256=6MH1yusfPNNa2RSbHhe48-WlUG1YJQsxMK2TkjemloI,1021
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cg/services/run_devices/pacbio/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py,sha256=
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cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py,sha256=dZWnssL1RgGkruPfKtJxZjghW1AGj8aiL4J4U7RorLE,4742
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cg/services/run_devices/pacbio/data_transfer_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py,sha256=
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cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py,sha256=XqJ6cJc2KfiI0svQFvZe8Hz4EcCDaggbvKkp6HBejag,2410
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cg/services/run_devices/pacbio/data_transfer_service/dto.py,sha256=g_7nrCLjQyEstLbR10v6cZV6hZnlCX2RQbPCFL8vAzE,2022
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cg/services/run_devices/pacbio/data_transfer_service/utils.py,sha256=xQR-Sty5HwvjBpQbyZvnNnCaJrbFSRvb6pbzABCWiHY,4300
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cg/services/run_devices/pacbio/housekeeper_service/models.py,sha256=F1c7dID12XiR4TcyRq4mhRB5gWZz430z0h7sHKcni00,153
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cg/services/run_devices/pacbio/housekeeper_service/pacbio_houskeeper_service.py,sha256=kR3vbxWoJ-axouCofLjgfLgKPgdryaMu7vgo-EU1emY,5354
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cg/services/run_devices/pacbio/metrics_parser/metrics_parser.py,sha256=26aAxw4xmBwtkVrSD4bmjThTTLsB6hmJgZEUXrITRW8,3279
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cg/services/run_devices/pacbio/metrics_parser/models.py,sha256=4BTxMv5d5eg2NSoBoZ8EwVqJyGuLTqHacgiSQ3AFL0E,7331
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cg/services/run_devices/pacbio/metrics_parser/utils.py,sha256=Y_Jsj-mnsuVF-iKZ7W1sJAuWqw25ayVonj9ktLHCNfA,3467
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cg/services/run_devices/pacbio/post_processing_service.py,sha256=0NOmLAzF3I2UHbyKDAcEFJL5XykPMBLxs2Dz40J-UTc,3962
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cg/services/run_devices/pacbio/run_data_generator/pacbio_run_data_generator.py,sha256=rvNepeIjt2BeZk-CvOpD449jmxceME0npEYAlqIebWg,1902
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@@ -842,7 +843,7 @@ cg/services/run_devices/pacbio/run_data_generator/run_data.py,sha256=si-F7CCwmIF
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cg/services/run_devices/pacbio/run_file_manager/models.py,sha256=C6kycBPx6YKNq2oFJOIhdrcPloi3QIBOrlbaAgeYzgs,192
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cg/services/run_devices/pacbio/run_file_manager/run_file_manager.py,sha256=xW8cKrLKh445hQnmtuIrvg6INs2lMSaDirG83fvimI4,5068
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cg/services/run_devices/pacbio/run_validator/pacbio_run_validator.py,sha256=d8fvmJcByEFPMnwqOe6mQsXXIO87WkXwfK9L_Bx7whg,3037
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cg/services/run_devices/pacbio/sequencing_runs_service.py,sha256=
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cg/services/run_devices/pacbio/sequencing_runs_service.py,sha256=nLT8uCSztpgS-G8J1m16BBeJi4x_NMddMw1hS0Ook2w,2139
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cg/services/run_devices/run_names/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/run_devices/run_names/service.py,sha256=y2ljpN_gGew6grIHnez740IW6cOzyyz0sWS_O9Jut68,288
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@@ -852,9 +853,9 @@ cg/services/sample_run_metrics_service/dtos.py,sha256=bJ0BL-QkqXIAAIg3F9edIdzAa_
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cg/services/sample_run_metrics_service/sample_run_metrics_service.py,sha256=aQvOuorTG97lUbw7OREO8nsPhO3ouQ38RwksstGwguQ,1795
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cg/services/sample_run_metrics_service/utils.py,sha256=BwICxptnhGg8oBghCLhzHaMNu0LuEV40cSYz1e8mB0A,829
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cg/services/sequencing_qc_service/__init__.py,sha256=OaL9dyyI6B8uRjopTIoD1zcX_H-SbGj46ZM-V-aoq6w,88
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cg/services/sequencing_qc_service/quality_checks/checks.py,sha256=
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cg/services/sequencing_qc_service/quality_checks/checks.py,sha256=Dew1xNjUBShAgv-kZtHNIL4HK6sMicu-cgACeeDjy20,2523
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cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=JCP__el8dflPuSE0QUea4NdRz_9XWu5l254VizNAy-U,7945
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cg/services/sequencing_qc_service/sequencing_qc_service.py,sha256=2QIJ9IDZeMtO74ZHJ9bfzyK3-RhDK-m9xaoKsi9RHt8,1969
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cg/services/sequencing_qc_service/utils.py,sha256=5WHJltBICfRODEzFVPFTdCbGNaMKCaVeOswHgIOGgFc,199
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cg/services/slurm_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/services/slurm_service/slurm_cli_service.py,sha256=t-XZoAOPgL-eufwK0A6H8WJvGtfWnlIYxnvKZJIX5-Y,702
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@@ -874,10 +875,10 @@ cg/store/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/store/api/data_classes.py,sha256=vgJehK0zm3SdB4LAQAWvTjoCHfos4N8_Vf0DDshrAnM,289
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cg/store/base.py,sha256=qmIjuWuq_wryBfGoSZny9nvqZj7Hl8N23hcdQ7Hss5I,6885
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cg/store/crud/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cg/store/crud/create.py,sha256=
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cg/store/crud/delete.py,sha256=TlpoVWvUQMaRfy5bk-icFf9SSi_0Ir6XpFcAiM22DB0,1386
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cg/store/crud/update.py,sha256=FZvOPebNnkWICu1N4gTdFeiMcuTUPglgCDfaxE6G288,6262
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cg/store/database.py,sha256=7B0hZpMSKtu5R885TSI4UBj8id1T5JNBY-tn69n6Fk0,1662
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cg/store/exc.py,sha256=uUCywNSwGus2uZnqmN56LHV84fHfkFYo8jXms1ToCnQ,274
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cg/store/filters/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -903,8 +904,8 @@ cg/store/filters/status_panel_filters.py,sha256=qMYhIsrF9G3mjCvL9b9O2l_cmD3SfPWh
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cg/store/filters/status_pool_filters.py,sha256=XcYqe2z5k_q09xpp4cleDMQ4Q3o2y7UPCkB0QUkl1ck,4308
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cg/store/filters/status_sample_filters.py,sha256=mRpt_ik7niMjBo9K7pP8cmdfDMdr0B3I6Tt2MWXkLoc,9656
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cg/store/filters/status_user_filters.py,sha256=sMwKeWqgEtqv8gyhbN_Uf5huPUxbOt5qEqMWVu67Zys,1328
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cg/store/models.py,sha256=
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cg/store/models.py,sha256=dSJRWdvqFmgIbYTlQbsZD8utH10BIjbtUKERybnlssI,43915
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cg/store/store.py,sha256=mz1TfKPlanH2uQyhZdwe_8VKg0IdFolmromKLu668IY,630
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cg/utils/__init__.py,sha256=gGjdV2l_hfWFCTybU6dwDk_FcItM88EIHNPaX6g1qUk,30
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cg/utils/calculations.py,sha256=zLVJO6nNw6n7AW7fHZI56UnQ23lqJrShB4Hh2ow6-TQ,349
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cg/utils/checksum/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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@@ -922,7 +923,7 @@ cg/utils/flask/enum.py,sha256=xwNVtFPkSzoloJctLHu7obRyxcng1GJrhkeYkqwf9tw,1052
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cg/utils/time.py,sha256=_VOglhrFEZ5cwHK1U1g36SdwzB7UvV-Nvlt4ymuZUho,1501
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cg/utils/utils.py,sha256=RciI_UhWcnG_pMZrmQZ1ZYb-O1N0DweTYMmhE0SIRgQ,1410
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cg-83.14.0.dist-info/METADATA,sha256=NfSMZZpwQzFwb2vRaPhpKv6sY5l3gfuNbeDIL81JQyk,4940
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cg-83.14.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
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cg-83.14.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
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cg-83.14.0.dist-info/RECORD,,
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