MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
cg/__init__.py
cg/exc.py
cg.egg-info/PKG-INFO
cg.egg-info/SOURCES.txt
cg.egg-info/dependency_links.txt
cg.egg-info/entry_points.txt
cg.egg-info/not-zip-safe
cg.egg-info/requires.txt
cg.egg-info/top_level.txt
cg/apps/__init__.py
cg/apps/environ.py
cg/apps/gt.py
cg/apps/loqus.py
cg/apps/mutacc_auto.py
cg/apps/osticket.py
cg/apps/vogue.py
cg/apps/cgstats/__init__.py
cg/apps/cgstats/demux_sample.py
cg/apps/cgstats/dragen_demux_sample.py
cg/apps/cgstats/stats.py
cg/apps/cgstats/crud/__init__.py
cg/apps/cgstats/crud/create.py
cg/apps/cgstats/crud/delete.py
cg/apps/cgstats/crud/find.py
cg/apps/cgstats/db/__init__.py
cg/apps/cgstats/db/models/__init__.py
cg/apps/cgstats/db/models/backup.py
cg/apps/cgstats/db/models/backup_tape.py
cg/apps/cgstats/db/models/base.py
cg/apps/cgstats/db/models/datasource.py
cg/apps/cgstats/db/models/demux.py
cg/apps/cgstats/db/models/flowcell.py
cg/apps/cgstats/db/models/project.py
cg/apps/cgstats/db/models/sample.py
cg/apps/cgstats/db/models/support_params.py
cg/apps/cgstats/db/models/unaligned.py
cg/apps/cgstats/db/models/version.py
cg/apps/cgstats/parsers/__init__.py
cg/apps/cgstats/parsers/adapter_metrics.py
cg/apps/cgstats/parsers/conversion_stats.py
cg/apps/cgstats/parsers/demux_stats.py
cg/apps/cgstats/parsers/dragen_demultiplexing_stats.py
cg/apps/cgstats/parsers/run_info.py
cg/apps/coverage/__init__.py
cg/apps/coverage/api.py
cg/apps/crunchy/__init__.py
cg/apps/crunchy/crunchy.py
cg/apps/crunchy/files.py
cg/apps/crunchy/sbatch.py
cg/apps/demultiplex/__init__.py
cg/apps/demultiplex/demultiplex_api.py
cg/apps/demultiplex/demux_report.py
cg/apps/demultiplex/sbatch.py
cg/apps/demultiplex/sample_sheet/__init__.py
cg/apps/demultiplex/sample_sheet/create.py
cg/apps/demultiplex/sample_sheet/dummy_sample.py
cg/apps/demultiplex/sample_sheet/index.py
cg/apps/demultiplex/sample_sheet/novaseq_sample_sheet.py
cg/apps/hermes/__init__.py
cg/apps/hermes/hermes_api.py
cg/apps/hermes/models.py
cg/apps/housekeeper/__init__.py
cg/apps/housekeeper/hk.py
cg/apps/housekeeper/models.py
cg/apps/invoice/__init__.py
cg/apps/invoice/render.py
cg/apps/invoice/templates/KI_pool_invoice.xlsx
cg/apps/invoice/templates/KI_sample_invoice.xlsx
cg/apps/invoice/templates/KTH_pool_invoice.xlsx
cg/apps/invoice/templates/KTH_sample_invoice.xlsx
cg/apps/lims/__init__.py
cg/apps/lims/api.py
cg/apps/lims/batch.py
cg/apps/lims/order.py
cg/apps/lims/samplesheet.py
cg/apps/madeline/__init__.py
cg/apps/madeline/api.py
cg/apps/mip/__init__.py
cg/apps/mip/confighandler.py
cg/apps/orderform/__init__.py
cg/apps/orderform/excel_orderform_parser.py
cg/apps/orderform/json_orderform_parser.py
cg/apps/orderform/orderform_parser.py
cg/apps/scout/__init__.py
cg/apps/scout/scout_export.py
cg/apps/scout/scoutapi.py
cg/apps/shipping/__init__.py
cg/apps/shipping/shipping_api.py
cg/apps/slurm/__init__.py
cg/apps/slurm/sbatch.py
cg/apps/slurm/slurm_api.py
cg/apps/tb/__init__.py
cg/apps/tb/api.py
cg/apps/tb/models.py
cg/cli/__init__.py
cg/cli/add.py
cg/cli/backup.py
cg/cli/base.py
cg/cli/clean.py
cg/cli/export.py
cg/cli/get.py
cg/cli/import_cmd.py
cg/cli/reset.py
cg/cli/status.py
cg/cli/transfer.py
cg/cli/compress/__init__.py
cg/cli/compress/base.py
cg/cli/compress/fastq.py
cg/cli/compress/helpers.py
cg/cli/delete/__init__.py
cg/cli/delete/base.py
cg/cli/delete/case.py
cg/cli/delete/cases.py
cg/cli/deliver/__init__.py
cg/cli/deliver/base.py
cg/cli/demultiplex/__init__.py
cg/cli/demultiplex/add.py
cg/cli/demultiplex/base.py
cg/cli/demultiplex/demux.py
cg/cli/demultiplex/finish.py
cg/cli/demultiplex/report.py
cg/cli/demultiplex/sample_sheet.py
cg/cli/deploy/__init__.py
cg/cli/deploy/base.py
cg/cli/generate/__init__.py
cg/cli/generate/base.py
cg/cli/generate/commands.py
cg/cli/generate/balsamic/__init__.py
cg/cli/generate/balsamic/base.py
cg/cli/generate/mip_dna/__init__.py
cg/cli/generate/mip_dna/base.py
cg/cli/set/__init__.py
cg/cli/set/base.py
cg/cli/set/families.py
cg/cli/set/family.py
cg/cli/store/__init__.py
cg/cli/store/fastq.py
cg/cli/store/store.py
cg/cli/upload/__init__.py
cg/cli/upload/base.py
cg/cli/upload/clinical_delivery.py
cg/cli/upload/coverage.py
cg/cli/upload/delivery_report.py
cg/cli/upload/fohm.py
cg/cli/upload/genotype.py
cg/cli/upload/gisaid.py
cg/cli/upload/mutacc.py
cg/cli/upload/observations.py
cg/cli/upload/scout.py
cg/cli/upload/utils.py
cg/cli/upload/validate.py
cg/cli/upload/vogue.py
cg/cli/upload/nipt/__init__.py
cg/cli/upload/nipt/base.py
cg/cli/upload/nipt/ftp.py
cg/cli/upload/nipt/statina.py
cg/cli/workflow/__init__.py
cg/cli/workflow/base.py
cg/cli/workflow/commands.py
cg/cli/workflow/balsamic/__init__.py
cg/cli/workflow/balsamic/base.py
cg/cli/workflow/balsamic/options.py
cg/cli/workflow/balsamic/qc.py
cg/cli/workflow/balsamic/umi.py
cg/cli/workflow/fastq/__init__.py
cg/cli/workflow/fastq/base.py
cg/cli/workflow/fluffy/__init__.py
cg/cli/workflow/fluffy/base.py
cg/cli/workflow/microsalt/__init__.py
cg/cli/workflow/microsalt/base.py
cg/cli/workflow/mip/__init__.py
cg/cli/workflow/mip/base.py
cg/cli/workflow/mip/options.py
cg/cli/workflow/mip_dna/__init__.py
cg/cli/workflow/mip_dna/base.py
cg/cli/workflow/mip_rna/__init__.py
cg/cli/workflow/mip_rna/base.py
cg/cli/workflow/mutant/__init__.py
cg/cli/workflow/mutant/base.py
cg/constants/__init__.py
cg/constants/cgstats.py
cg/constants/compression.py
cg/constants/constants.py
cg/constants/delivery.py
cg/constants/demultiplexing.py
cg/constants/encryption.py
cg/constants/extraction.py
cg/constants/gene_panel.py
cg/constants/indexes.py
cg/constants/lims.py
cg/constants/loqus_upload.py
cg/constants/nipt.py
cg/constants/orderforms.py
cg/constants/paths.py
cg/constants/pdc.py
cg/constants/pedigree.py
cg/constants/priority.py
cg/constants/process.py
cg/constants/report.py
cg/constants/sample_sources.py
cg/constants/scout_upload.py
cg/constants/sequencing.py
cg/constants/subject.py
cg/constants/symbols.py
cg/constants/tags.py
cg/constants/tb.py
cg/meta/__init__.py
cg/meta/deliver.py
cg/meta/deliver_ticket.py
cg/meta/invoice.py
cg/meta/meta.py
cg/meta/backup/__init__.py
cg/meta/backup/backup.py
cg/meta/backup/pdc.py
cg/meta/clean/__init__.py
cg/meta/clean/api.py
cg/meta/clean/demultiplexed_flow_cells.py
cg/meta/clean/flow_cell_run_directories.py
cg/meta/compress/__init__.py
cg/meta/compress/compress.py
cg/meta/compress/files.py
cg/meta/demultiplex/__init__.py
cg/meta/demultiplex/delete_demultiplex_api.py
cg/meta/demultiplex/demux_post_processing.py
cg/meta/demultiplex/files.py
cg/meta/encryption/__init__.py
cg/meta/encryption/encryption.py
cg/meta/orders/__init__.py
cg/meta/orders/api.py
cg/meta/orders/balsamic_qc_submitter.py
cg/meta/orders/balsamic_submitter.py
cg/meta/orders/balsamic_umi_submitter.py
cg/meta/orders/case_submitter.py
cg/meta/orders/fastq_submitter.py
cg/meta/orders/fluffy_submitter.py
cg/meta/orders/lims.py
cg/meta/orders/metagenome_submitter.py
cg/meta/orders/microbial_submitter.py
cg/meta/orders/microsalt_submitter.py
cg/meta/orders/mip_dna_submitter.py
cg/meta/orders/mip_rna_submitter.py
cg/meta/orders/pool_submitter.py
cg/meta/orders/rml_submitter.py
cg/meta/orders/sars_cov_2_submitter.py
cg/meta/orders/submitter.py
cg/meta/orders/ticket_handler.py
cg/meta/report/__init__.py
cg/meta/report/api.py
cg/meta/report/balsamic.py
cg/meta/report/balsamic_umi.py
cg/meta/report/field_validators.py
cg/meta/report/mip_dna.py
cg/meta/report/templates/balsamic_report.html
cg/meta/report/templates/bootstrap.html
cg/meta/report/templates/mip-dna_report.html
cg/meta/rsync/__init__.py
cg/meta/rsync/rsync_api.py
cg/meta/rsync/sbatch.py
cg/meta/tar/__init__.py
cg/meta/tar/tar.py
cg/meta/transfer/__init__.py
cg/meta/transfer/external_data.py
cg/meta/transfer/flowcell.py
cg/meta/transfer/lims.py
cg/meta/upload/__init__.py
cg/meta/upload/coverage.py
cg/meta/upload/gt.py
cg/meta/upload/mutacc.py
cg/meta/upload/observations.py
cg/meta/upload/upload_api.py
cg/meta/upload/vogue.py
cg/meta/upload/balsamic/__init__.py
cg/meta/upload/balsamic/balsamic.py
cg/meta/upload/fohm/__init__.py
cg/meta/upload/fohm/fohm.py
cg/meta/upload/gisaid/__init__.py
cg/meta/upload/gisaid/constants.py
cg/meta/upload/gisaid/gisaid.py
cg/meta/upload/gisaid/models.py
cg/meta/upload/mip_dna/__init__.py
cg/meta/upload/mip_dna/mip_dna.py
cg/meta/upload/nipt/__init__.py
cg/meta/upload/nipt/models.py
cg/meta/upload/nipt/nipt.py
cg/meta/upload/scout/__init__.py
cg/meta/upload/scout/balsamic_config_builder.py
cg/meta/upload/scout/balsamic_umi_config_builder.py
cg/meta/upload/scout/hk_tags.py
cg/meta/upload/scout/mip_config_builder.py
cg/meta/upload/scout/scout_config_builder.py
cg/meta/upload/scout/uploadscoutapi.py
cg/meta/workflow/__init__.py
cg/meta/workflow/analysis.py
cg/meta/workflow/balsamic.py
cg/meta/workflow/balsamic_qc.py
cg/meta/workflow/balsamic_umi.py
cg/meta/workflow/fastq.py
cg/meta/workflow/fluffy.py
cg/meta/workflow/microsalt.py
cg/meta/workflow/mip.py
cg/meta/workflow/mip_dna.py
cg/meta/workflow/mip_rna.py
cg/meta/workflow/mutant.py
cg/meta/workflow/prepare_fastq.py
cg/models/__init__.py
cg/models/analysis.py
cg/models/cg_config.py
cg/models/compression_data.py
cg/models/email.py
cg/models/file_data.py
cg/models/balsamic/__init__.py
cg/models/balsamic/analysis.py
cg/models/balsamic/config.py
cg/models/balsamic/metrics.py
cg/models/cgstats/__init__.py
cg/models/cgstats/flowcell.py
cg/models/cgstats/stats_sample.py
cg/models/deliverables/__init__.py
cg/models/deliverables/metric_deliverables.py
cg/models/demultiplex/__init__.py
cg/models/demultiplex/demux_results.py
cg/models/demultiplex/flowcell.py
cg/models/demultiplex/run_parameters.py
cg/models/demultiplex/sbatch.py
cg/models/lims/__init__.py
cg/models/lims/sample.py
cg/models/mip/__init__.py
cg/models/mip/mip_analysis.py
cg/models/mip/mip_config.py
cg/models/mip/mip_metrics_deliverables.py
cg/models/mip/mip_sample_info.py
cg/models/observations/__init__.py
cg/models/observations/observations_input_files.py
cg/models/orders/__init__.py
cg/models/orders/constants.py
cg/models/orders/excel_sample.py
cg/models/orders/json_sample.py
cg/models/orders/order.py
cg/models/orders/orderform_schema.py
cg/models/orders/sample_base.py
cg/models/orders/samples.py
cg/models/report/__init__.py
cg/models/report/metadata.py
cg/models/report/report.py
cg/models/report/sample.py
cg/models/report/validators.py
cg/models/scout/__init__.py
cg/models/scout/scout_load_config.py
cg/models/slurm/__init__.py
cg/models/slurm/sbatch.py
cg/models/workflow/__init__.py
cg/models/workflow/mutant.py
cg/resources/20181012_Indices.csv
cg/resources/__init__.py
cg/server/__init__.py
cg/server/admin.py
cg/server/api.py
cg/server/app.py
cg/server/auto.py
cg/server/config.py
cg/server/ext.py
cg/server/invoices/__init__.py
cg/server/invoices/views.py
cg/server/invoices/templates/invoices/index.html
cg/server/invoices/templates/invoices/invoice.html
cg/server/invoices/templates/invoices/layout.html
cg/server/invoices/templates/invoices/new.html
cg/server/templates/admin/index.html
cg/store/__init__.py
cg/store/models.py
cg/store/queries.py
cg/store/utils.py
cg/store/api/__init__.py
cg/store/api/add.py
cg/store/api/base.py
cg/store/api/core.py
cg/store/api/delete.py
cg/store/api/findbasicdata.py
cg/store/api/findbusinessdata.py
cg/store/api/import_func.py
cg/store/api/models.py
cg/store/api/reset.py
cg/store/api/status.py
cg/utils/__init__.py
cg/utils/commands.py
cg/utils/date.py
cg/utils/email.py
cg/utils/enums.py
cg/utils/files.py
cg/utils/time.py
cg/utils/checksum/__init__.py
cg/utils/checksum/checksum.py
cg/utils/click/EnumChoice.py
cg/utils/click/__init__.py
cg/utils/flask/__init__.py
cg/utils/flask/enum.py
tests/__init__.py
tests/conftest.py
tests/small_helpers.py
tests/store_helpers.py
tests/test_store_helpers.py
tests/apps/conftest.py
tests/apps/test_apps_environ.py
tests/apps/test_osticket.py
tests/apps/cgstats/conftest.py
tests/apps/cgstats/test_cgstats_create.py
tests/apps/cgstats/test_stats.py
tests/apps/cgstats/crud/test_create_novaseq.py
tests/apps/cgstats/crud/test_delete.py
tests/apps/cgstats/parsers/test_conversion_stats.py
tests/apps/cgstats/parsers/test_demux_stats.py
tests/apps/cgstats/parsers/test_run_info.py
tests/apps/coverage/test_coverage.py
tests/apps/crunchy/conftest.py
tests/apps/crunchy/test_compress_fastq.py
tests/apps/crunchy/test_config.py
tests/apps/crunchy/test_crunchy.py
tests/apps/crunchy/test_spring_decompression.py
tests/apps/demultiplex/__init__.py
tests/apps/demultiplex/conftest.py
tests/apps/demultiplex/test_convert_to_sample_sheet.py
tests/apps/demultiplex/test_parse_run_parameters.py
tests/apps/demultiplex/test_sample_sheet.py
tests/apps/gt/conftest.py
tests/apps/gt/test_gt_api.py
tests/apps/hk/conftest.py
tests/apps/hk/test__getattr__.py
tests/apps/hk/test_add_file.py
tests/apps/hk/test_bundles.py
tests/apps/hk/test_core.py
tests/apps/hk/test_file.py
tests/apps/hk/test_version.py
tests/apps/lims/conftest.py
tests/apps/lims/test_api.py
tests/apps/loqus/conftest.py
tests/apps/loqus/test_loqusdbapi.py
tests/apps/madeline/conftest.py
tests/apps/madeline/test_madeline.py
tests/apps/mip/conftest.py
tests/apps/mip/test_config_mip.py
tests/apps/mutacc_auto/conftest.py
tests/apps/mutacc_auto/test_mutacc_auto.py
tests/apps/orderform/conftest.py
tests/apps/orderform/test_excel_orderform_parser.py
tests/apps/orderform/test_excel_sample_schema.py
tests/apps/orderform/test_json_orderform_parser.py
tests/apps/orderform/test_orderform_parser.py
tests/apps/scout/conftest.py
tests/apps/scout/test_get_causative_variants.py
tests/apps/scout/test_get_scout_cases.py
tests/apps/scout/test_scout_load_config.py
tests/apps/scout/test_scout_models.py
tests/apps/shipping/conftest.py
tests/apps/shipping/test_shipping.py
tests/apps/slurm/conftest.py
tests/apps/slurm/test_slurm_api.py
tests/apps/vogue/conftest.py
tests/apps/vogue/test_vogue_api.py
tests/cli/__init__.py
tests/cli/conftest.py
tests/cli/test_base.py
tests/cli/test_cli_status_cases.py
tests/cli/add/__init__.py
tests/cli/add/test_cli_add.py
tests/cli/add/test_cli_add_family.py
tests/cli/add/test_cli_add_relationship.py
tests/cli/add/test_cli_add_sample.py
tests/cli/backup/__init__.py
tests/cli/backup/conftest.py
tests/cli/backup/test_backup_command.py
tests/cli/clean/conftest.py
tests/cli/clean/test_balsamic_clean.py
tests/cli/clean/test_clean_hk_bundle_files.py
tests/cli/clean/test_hk_bundle_files.py
tests/cli/clean/test_hk_case_bundle_files.py
tests/cli/clean/test_rsync_past_run_dirs.py
tests/cli/compress/conftest.py
tests/cli/compress/test_cli_compress_fastq.py
tests/cli/compress/test_cli_decompress_spring.py
tests/cli/compress/test_compress_helpers.py
tests/cli/compress/test_store_fastq.py
tests/cli/delete/test_case.py
tests/cli/delete/test_cases.py
tests/cli/deliver/conftest.py
tests/cli/deliver/test_deliver_base.py
tests/cli/deliver/test_rsync_base.py
tests/cli/deliver/test_run_deliver_cmd.py
tests/cli/demultiplex/__init__.py
tests/cli/demultiplex/conftest.py
tests/cli/demultiplex/test_add_flowcell.py
tests/cli/demultiplex/test_create_sample_sheet.py
tests/cli/demultiplex/test_demultiplex_flowcell.py
tests/cli/demultiplex/test_finish_demux.py
tests/cli/demultiplex/test_stats_command.py
tests/cli/demultiplex/test_validate_sample_sheet.py
tests/cli/deploy/conftest.py
tests/cli/deploy/test_deploy_command.py
tests/cli/generate/__init__.py
tests/cli/generate/test_cli_base.py
tests/cli/generate/mip-dna/__init__.py
tests/cli/generate/mip-dna/conftest.py
tests/cli/generate/mip-dna/test_cli_delivery_report.py
tests/cli/get/__init__.py
tests/cli/get/test_cli_get.py
tests/cli/get/test_cli_get_analysis.py
tests/cli/get/test_cli_get_family.py
tests/cli/get/test_cli_get_flowcell.py
tests/cli/get/test_cli_get_sample.py
tests/cli/set/conftest.py
tests/cli/set/test_families.py
tests/cli/set/test_family.py
tests/cli/set/test_flowcell.py
tests/cli/set/test_sample.py
tests/cli/set/test_samples.py
tests/cli/upload/__init__.py
tests/cli/upload/conftest.py
tests/cli/upload/test_cli_upload.py
tests/cli/upload/test_cli_upload_auto.py
tests/cli/upload/test_cli_upload_delivery_report.py
tests/cli/upload/test_cli_upload_fastq.py
tests/cli/upload/test_cli_upload_genotype.py
tests/cli/upload/test_cli_upload_nipt.py
tests/cli/upload/test_cli_upload_nipt_ftp.py
tests/cli/upload/test_cli_upload_nipt_statina.py
tests/cli/upload/test_cli_upload_vogue.py
tests/cli/workflow/__init__.py
tests/cli/workflow/conftest.py
tests/cli/workflow/test_cli_workflow.py
tests/cli/workflow/test_cli_workflow_clean.py
tests/cli/workflow/balsamic/conftest.py
tests/cli/workflow/balsamic/test_cli_balsamic_config_case.py
tests/cli/workflow/balsamic/test_compound_commands.py
tests/cli/workflow/balsamic/test_link.py
tests/cli/workflow/balsamic/test_report_deliver.py
tests/cli/workflow/balsamic/test_run.py
tests/cli/workflow/balsamic/test_store_housekeeper.py
tests/cli/workflow/fastq/__init__.py
tests/cli/workflow/fastq/test_fastq_base.py
tests/cli/workflow/fluffy/__init__.py
tests/cli/workflow/fluffy/conftest.py
tests/cli/workflow/fluffy/test_cli_create_samplesheet.py
tests/cli/workflow/fluffy/test_cli_link.py
tests/cli/workflow/fluffy/test_cli_run.py
tests/cli/workflow/fluffy/test_cli_start.py
tests/cli/workflow/fluffy/test_cli_store.py
tests/cli/workflow/microsalt/conftest.py
tests/cli/workflow/microsalt/test_microsalt_case_config.py
tests/cli/workflow/microsalt/test_microsalt_run.py
tests/cli/workflow/microsalt/snapshots/__init__.py
tests/cli/workflow/microsalt/snapshots/snap_test_microsalt_case_config.py
tests/cli/workflow/mip/conftest.py
tests/cli/workflow/mip/test_cli_mip_base.py
tests/cli/workflow/mip/test_cli_mip_dna_config_case.py
tests/cli/workflow/mip/test_cli_mip_dna_link.py
tests/cli/workflow/mip/test_cli_mip_dna_panel.py
tests/cli/workflow/mip/test_cli_mip_dna_run.py
tests/cli/workflow/mip/test_cli_mip_dna_start.py
tests/cli/workflow/mip/test_cli_mip_rna_config_case.py
tests/cli/workflow/mip/test_cli_mip_rna_link.py
tests/cli/workflow/mip/test_cli_mip_rna_run.py
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