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/pdc.py
cg/apps/vogue.py
cg/apps/cgstats/__init__.py
cg/apps/cgstats/demux_sample.py
cg/apps/cgstats/stats.py
cg/apps/cgstats/crud/__init__.py
cg/apps/cgstats/crud/create.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/conversion_stats.py
cg/apps/cgstats/parsers/demux_stats.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/mip/parse_qcmetrics.py
cg/apps/mip/parse_sampleinfo.py
cg/apps/mip/parse_trending.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/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/coverage.py
cg/cli/upload/delivery_report.py
cg/cli/upload/genotype.py
cg/cli/upload/gisaid.py
cg/cli/upload/mutacc.py
cg/cli/upload/nipt.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/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/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/store.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/gene_panel.py
cg/constants/lims.py
cg/constants/orderforms.py
cg/constants/paths.py
cg/constants/priority.py
cg/constants/process.py
cg/constants/sample_sources.py
cg/constants/scout_upload.py
cg/constants/symbols.py
cg/constants/tags.py
cg/meta/__init__.py
cg/meta/backup.py
cg/meta/deliver.py
cg/meta/invoice.py
cg/meta/meta.py
cg/meta/rsync.py
cg/meta/compress/__init__.py
cg/meta/compress/compress.py
cg/meta/compress/files.py
cg/meta/demultiplex/__init__.py
cg/meta/demultiplex/demux_post_processing.py
cg/meta/demultiplex/files.py
cg/meta/orders/__init__.py
cg/meta/orders/api.py
cg/meta/orders/lims.py
cg/meta/orders/schema.py
cg/meta/orders/status.py
cg/meta/orders/ticket_handler.py
cg/meta/report/__init__.py
cg/meta/report/api.py
cg/meta/report/presenter.py
cg/meta/report/report_helper.py
cg/meta/report/report_validator.py
cg/meta/report/sample_calculator.py
cg/meta/report/sample_helper.py
cg/meta/report/templates/bootstrap.html
cg/meta/report/templates/report.html
cg/meta/store/__init__.py
cg/meta/store/base.py
cg/meta/store/mip.py
cg/meta/transfer/__init__.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/vogue.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/nipt/__init__.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/hk_tags.py
cg/meta/upload/scout/mip_config_builder.py
cg/meta/upload/scout/scout_config_builder.py
cg/meta/upload/scout/scoutapi.py
cg/meta/workflow/__init__.py
cg/meta/workflow/analysis.py
cg/meta/workflow/balsamic.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/cg_config.py
cg/models/compression_data.py
cg/models/file_data.py
cg/models/cgstats/__init__.py
cg/models/cgstats/flowcell.py
cg/models/cgstats/stats_sample.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/orders/__init__.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/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/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/StrEnum.py
cg/utils/__init__.py
cg/utils/commands.py
cg/utils/date.py
cg/utils/files.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/crud/test_create_novaseq.py
tests/apps/cgstats/parsers/test_conversion_stats.py
tests/apps/cgstats/parsers/test_demux_stats.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_apps_mip_files.py
tests/apps/mip/test_config_mip.py
tests/apps/mip/snapshots/__init__.py
tests/apps/mip/snapshots/snap_test_apps_mip_files.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/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/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.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/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_genotype.py
tests/cli/upload/test_cli_upload_nipt.py
tests/cli/upload/test_cli_upload_vogue.py
tests/cli/workflow/conftest.py
tests/cli/workflow/test_cli_workflow.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/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_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
tests/cli/workflow/mip/test_cli_mip_store.py
tests/fixtures/DEMUX/160219_D00410_0217_AHJKMYBCXX/runParameters.xml
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tests/fixtures/analysis/sample_coverage.bed
tests/fixtures/analysis/balsamic/tn_panel/adm1.cram
tests/fixtures/analysis/balsamic/tn_panel/snv.vcf
tests/fixtures/analysis/balsamic/tn_panel/sv.vcf
tests/fixtures/analysis/mip/dna/adm1.cram
tests/fixtures/analysis/mip/dna/adm1.mt.bam
tests/fixtures/analysis/mip/dna/multiqc.html
tests/fixtures/analysis/mip/dna/report.pdf
tests/fixtures/analysis/mip/dna/smn.vcf
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tests/fixtures/analysis/mip/dna/snv_research.vcf
tests/fixtures/analysis/mip/dna/str.vcf
tests/fixtures/analysis/mip/dna/sv.vcf
tests/fixtures/analysis/mip/dna/sv_research.vcf
tests/fixtures/analysis/mip/dna/vcf2cytosure.txt
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tests/fixtures/apps/balsamic/case/metadata_directory.yml
tests/fixtures/apps/balsamic/case/metadata_file_tags.yml
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tests/fixtures/apps/demultiplexing/runParameters_missing_flowcell_run_field.xml
tests/fixtures/apps/demultiplexing/unknown_run_parameters.xml
tests/fixtures/apps/demultiplexing/201203_A00689_0200_AHVKJCDRXX/RunParameters.xml
tests/fixtures/apps/demultiplexing/201203_A00689_0200_AHVKJCDRXX/SampleSheet.csv
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