MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
cg/__init__.py
cg/constants.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/hk.py
cg/apps/loqus.py
cg/apps/madeline.py
cg/apps/mutacc_auto.py
cg/apps/osticket.py
cg/apps/pdc.py
cg/apps/scoutapi.py
cg/apps/stats.py
cg/apps/vogue.py
cg/apps/balsamic/__init__.py
cg/apps/balsamic/api.py
cg/apps/balsamic/fastq.py
cg/apps/coverage/__init__.py
cg/apps/coverage/api.py
cg/apps/crunchy/__init__.py
cg/apps/crunchy/crunchy.py
cg/apps/crunchy/models.py
cg/apps/crunchy/sbatch.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/constants.py
cg/apps/lims/limsjson.py
cg/apps/lims/order.py
cg/apps/lims/orderform.py
cg/apps/madeline/__init__.py
cg/apps/madeline/api.py
cg/apps/microsalt/__init__.py
cg/apps/microsalt/fastq.py
cg/apps/mip/__init__.py
cg/apps/mip/base.py
cg/apps/mip/confighandler.py
cg/apps/mip_rna/__init__.py
cg/apps/mip_rna/files.py
cg/apps/pipelines/__init__.py
cg/apps/pipelines/fastqhandler.py
cg/apps/tb/__init__.py
cg/apps/tb/api.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/set.py
cg/cli/status.py
cg/cli/store.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/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/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/workflow/__init__.py
cg/cli/workflow/base.py
cg/cli/workflow/get_links.py
cg/cli/workflow/balsamic/__init__.py
cg/cli/workflow/balsamic/base.py
cg/cli/workflow/balsamic/deliver.py
cg/cli/workflow/microsalt/__init__.py
cg/cli/workflow/microsalt/base.py
cg/cli/workflow/microsalt/deliver.py
cg/cli/workflow/microsalt/store.py
cg/cli/workflow/mip/__init__.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_dna/deliver.py
cg/cli/workflow/mip_rna/__init__.py
cg/cli/workflow/mip_rna/base.py
cg/cli/workflow/mip_rna/deliver.py
cg/meta/__init__.py
cg/meta/backup.py
cg/meta/deliver.py
cg/meta/invoice.py
cg/meta/compress/__init__.py
cg/meta/compress/compress.py
cg/meta/compress/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/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/scoutapi.py
cg/meta/upload/vogue.py
cg/meta/workflow/__init__.py
cg/meta/workflow/balsamic.py
cg/meta/workflow/microsalt.py
cg/meta/workflow/mip.py
cg/models/__init__.py
cg/models/compression_data.py
cg/models/file_data.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/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/reset.py
cg/store/api/status.py
cg/store/get/__init__.py
cg/store/get/cases.py
cg/utils/__init__.py
cg/utils/commands.py
cg/utils/date.py
cg/utils/files.py
tests/__init__.py
tests/conftest.py
tests/small_helpers.py
tests/store_helpers.py
tests/apps/conftest.py
tests/apps/test_apps_environ.py
tests/apps/test_osticket.py
tests/apps/balsamic/conftest.py
tests/apps/balsamic/test_fastqfileconcatenator.py
tests/apps/balsamic/test_fastqfilenamecreator.py
tests/apps/balsamic/test_fastqhandler.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/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_apps_lims_api.py
tests/apps/lims/test_apps_lims_orderform.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_base.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/usalt/conftest.py
tests/apps/usalt/test_usalt_fastqfilenamecreator.py
tests/apps/usalt/test_usalt_fastqhandler.py
tests/apps/vogue/conftest.py
tests/apps/vogue/test_vogue_api.py
tests/cli/conftest.py
tests/cli/test_base.py
tests/cli/test_cli_add.py
tests/cli/test_cli_add_family.py
tests/cli/test_cli_add_relationship.py
tests/cli/test_cli_add_sample.py
tests/cli/test_cli_get.py
tests/cli/test_cli_get_flowcell.py
tests/cli/test_cli_get_sample.py
tests/cli/test_cli_status_cases.py
tests/cli/clean/conftest.py
tests/cli/clean/test_balsamic_clean.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/set/conftest.py
tests/cli/set/test_family.py
tests/cli/set/test_flowcell.py
tests/cli/set/test_sample.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_scout.py
tests/cli/upload/test_cli_upload_vogue.py
tests/cli/workflow/conftest.py
tests/cli/workflow/test_cli_workflow.py
tests/cli/workflow/test_get_links.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/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_dna_run.py
tests/cli/workflow/mip/test_cli_mip_dna_start.py
tests/cli/workflow/mip/test_cli_mip_rna_run.py
tests/fixtures/DEMUX/160219_D00410_0217_AHJKMYBCXX/Unaligned5/Project_337334/Sample_ADM1136A3_XTC08/ADM1136A3_XTC08_AGTGGTCA_L001_R1_001.fastq.gz
tests/fixtures/DEMUX/160219_D00410_0217_AHJKMYBCXX/Unaligned5/Project_337334/Sample_ADM1136A3_XTC08/ADM1136A3_XTC08_AGTGGTCA_L001_R2_001.fastq.gz
tests/fixtures/DEMUX/160219_D00410_0217_AHJKMYBCXX/Unaligned5/Project_337334/Sample_ADM1136A3_XTC08/ADM1136A3_XTC08_AGTGGTCA_L002_R1_001.fastq.gz
tests/fixtures/DEMUX/160219_D00410_0217_AHJKMYBCXX/Unaligned5/Project_337334/Sample_ADM1136A3_XTC08/ADM1136A3_XTC08_AGTGGTCA_L002_R2_001.fastq.gz
tests/fixtures/analysis/sample_coverage.bed
tests/fixtures/apps/balsamic/case/config.json
tests/fixtures/apps/balsamic/case/metadata.yml
tests/fixtures/apps/balsamic/case/metadata_directory.yml
tests/fixtures/apps/balsamic/case/metadata_file_tags.yml
tests/fixtures/apps/crunchy/spring_metadata.json
tests/fixtures/apps/madeline/madeline.xml
tests/fixtures/apps/mip/dna/store/bundle_data.yaml
tests/fixtures/apps/mip/dna/store/case_config.yaml
tests/fixtures/apps/mip/dna/store/case_id_deliverables.yaml
tests/fixtures/apps/mip/dna/store/case_qc_sample_info.yaml
tests/fixtures/apps/mip/rna/case_config.yaml
tests/fixtures/apps/mip/rna/case_qc_sampleinfo.yaml
tests/fixtures/apps/mip/rna/store/bundle_data.yaml
tests/fixtures/apps/mip/rna/store/case_config.yaml
tests/fixtures/apps/mip/rna/store/case_id_deliverables.yaml
tests/fixtures/apps/mip/rna/store/case_qc_sample_info.yaml
tests/fixtures/apps/scout/643594.config.yaml
tests/fixtures/apps/tb/case/case_config.yaml
tests/fixtures/apps/tb/case/case_qc_metrics.yaml
tests/fixtures/apps/tb/case/case_qc_sample_info.yaml
tests/fixtures/fastq/dummy_run_R1_001.fastq.gz
tests/fixtures/fastq/fastq_run_R1_001.fastq.gz
tests/fixtures/fastq/fastq_run_R2_001.fastq.gz
tests/fixtures/orderforms/1508.21.balsamic.xlsx
tests/fixtures/orderforms/1508.21.fastq.xlsx
tests/fixtures/orderforms/1508.21.mip.xlsx
tests/fixtures/orderforms/1508.21.mip_balsamic.xlsx
tests/fixtures/orderforms/1508.21.mip_rna.xlsx
tests/fixtures/orderforms/1541.6.external.xlsx
tests/fixtures/orderforms/1603.9.microbial.xlsx
tests/fixtures/orderforms/1604.9.rml.xlsx
tests/fixtures/orderforms/1605.8.metagenome.xlsx
tests/fixtures/orderforms/~$1508.20.mip_rna.xlsx
tests/fixtures/orders/balsamic.json
tests/fixtures/orders/external.json
tests/fixtures/orders/fastq.json
tests/fixtures/orders/metagenome.json
tests/fixtures/orders/microbial.json
tests/fixtures/orders/mip.json
tests/fixtures/orders/mip_balsamic.json
tests/fixtures/orders/mip_rna.json
tests/fixtures/orders/rml.json
tests/fixtures/report/case_data.json
tests/fixtures/report/lims_exported_samples.json
tests/fixtures/report/lims_family.json
tests/fixtures/store/api/application_versions.xlsx
tests/fixtures/store/api/applications.xlsx
tests/meta/conftest.py
tests/meta/test_meta_mip_dna.py
tests/meta/compress/conftest.py
tests/meta/compress/test_clean_fastq.py
tests/meta/compress/test_compress_common.py
tests/meta/compress/test_compress_files.py
tests/meta/compress/test_compress_meta_fastq.py
tests/meta/compress/test_decompress_spring_meta.py
tests/meta/compress/test_meta_compress_update_hk.py
tests/meta/deliver/test_delivery_api.py
tests/meta/orders/conftest.py
tests/meta/orders/test_meta_orders_api.py
tests/meta/orders/test_meta_orders_lims.py
tests/meta/orders/test_meta_orders_status.py
tests/meta/report/conftest.py
tests/meta/report/test_presenter.py
tests/meta/report/test_report_api.py
tests/meta/report/test_report_helper.py
tests/meta/report/test_report_validator.py
tests/meta/report/test_sample_calculator.py
tests/meta/store/__init__.py
tests/meta/store/conftest.py
tests/meta/store/test_cg_meta_store_base.py
tests/meta/store/test_cg_meta_store_mip.py
tests/meta/store/snapshots/__init__.py
tests/meta/store/snapshots/snap_test_cg_meta_store_base.py
tests/meta/store/snapshots/snap_test_cg_meta_store_mip.py
tests/meta/transfer/conftest.py
tests/meta/transfer/test_meta_transfer_flowcell.py
tests/meta/transfer/test_meta_transfer_lims.py
tests/meta/upload/conftest.py
tests/meta/upload/test_meta_upload_coverage.py
tests/meta/upload/test_meta_upload_mutacc.py
tests/meta/upload/test_meta_upload_observations.py
tests/meta/upload/test_meta_upload_scoutapi.py
tests/meta/upload/vogue/conftest.py
tests/meta/upload/vogue/test_upload_vogue.py
tests/mocks/__init__.py
tests/mocks/crunchy.py
tests/mocks/hk_mock.py
tests/mocks/limsmock.py
tests/mocks/madeline.py
tests/mocks/scout.py
tests/models/conftest.py
tests/models/test_compression_data.py
tests/models/test_file_data.py
tests/server/conftest.py
tests/server/test_server_app.py
tests/server/test_server_auto.py
tests/store/conftest.py
tests/store/test_delivery.py
tests/store/test_store_models.py
tests/store/test_store_utils.py
tests/store/api/conftest.py
tests/store/api/test_store_add.py
tests/store/api/test_store_api_status.py
tests/store/api/test_store_api_status_analysis.py
tests/store/api/test_store_api_status_cases.py
tests/store/api/test_store_import_func.py
tests/store/api/test_store_reset.py
tests/store/api/status/test_analyses_to_clean.py
tests/store/api/status/test_analyses_to_delivery_report.py
tests/utils/__init__.py
tests/utils/conftest.py
tests/utils/test_commands.py