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Clinical-Genomics / cg

Glue between Clinical Genomics apps
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Inconsistent database models #1869

Closed seallard closed 1 year ago

seallard commented 1 year ago

Description

Some models and fields have unexpected names or have fields that are not used. Creating this issue to keep track of them.

Suggested solution

Rename fields, create migrations, apply migrations.

This can be closed when

Describe what needs to be done for this issue to be closed

Blocked by

If there are any blocking issues/prs/things in this or other repos. Please link to them.

seallard commented 1 year ago

These fields were flagged as not used and might be possible to remove: Generated with vulture --exclude tests,alembic,build . > output.txt

cg/apps/cgstats/db/models/datasource.py:16: unused variable 'rundate' (60% confidence)
cg/apps/cgstats/db/models/datasource.py:18: unused variable 'document_type' (60% confidence)
cg/apps/cgstats/db/models/flowcell.py:12: unused variable 'flowcell_pos' (60% confidence)
cg/apps/cgstats/db/models/sample.py:13: unused variable 'customerid' (60% confidence)
cg/apps/cgstats/db/models/sample.py:14: unused variable 'limsid' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:12: unused variable 'systempid' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:13: unused variable 'systemos' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:14: unused variable 'systemperlv' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:15: unused variable 'systemperlexe' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:16: unused variable 'idstring' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:18: unused variable 'commandline' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:19: unused variable 'sampleconfig_path' (60% confidence)
cg/apps/cgstats/db/models/support_params.py:20: unused variable 'sampleconfig' (60% confidence)
cg/apps/cgstats/db/models/unaligned.py:15: unused variable 'passed_filter_pct' (60% confidence)
cg/apps/cgstats/db/models/unaligned.py:17: unused variable 'raw_clusters_per_lane_pct' (60% confidence) cg/apps/tb/models.py:23: unused variable 'is_deleted' (60% confidence)
cg/apps/tb/models.py:26: unused variable 'user_id' (60% confidence) cg/apps/tb/models.py:47: unused variable 'extra' (60% confidence)
cg/apps/tb/models.py:48: unused variable 'validate_all' (60% confidence) cg/meta/upload/gisaid/models.py:40: unused variable 'fn' (60% confidence)
cg/meta/upload/gisaid/models.py:41: unused variable 'covv_collection_date' (60% confidence)
cg/meta/upload/gisaid/models.py:42: unused variable 'covv_subm_sample_id' (60% confidence)
cg/meta/upload/gisaid/models.py:44: unused variable 'covv_orig_lab' (60% confidence)
cg/meta/upload/gisaid/models.py:45: unused variable 'covv_type' (60% confidence)
cg/meta/upload/gisaid/models.py:46: unused variable 'covv_passage' (60% confidence)
cg/meta/upload/gisaid/models.py:47: unused variable 'covv_location' (60% confidence)
cg/meta/upload/gisaid/models.py:48: unused variable 'covv_host' (60% confidence)
cg/meta/upload/gisaid/models.py:49: unused variable 'covv_gender' (60% confidence)
cg/meta/upload/gisaid/models.py:50: unused variable 'covv_patient_age' (60% confidence)
cg/meta/upload/gisaid/models.py:51: unused variable 'covv_patient_status' (60% confidence)
cg/meta/upload/gisaid/models.py:52: unused variable 'covv_seq_technology' (60% confidence)
cg/meta/upload/gisaid/models.py:53: unused variable 'covv_orig_lab_addr' (60% confidence)
cg/meta/upload/gisaid/models.py:54: unused variable 'covv_subm_lab' (60% confidence)
cg/meta/upload/gisaid/models.py:55: unused variable 'covv_subm_lab_addr' (60% confidence)
cg/meta/upload/gisaid/models.py:56: unused variable 'covv_authors' (60% confidence) cg/meta/upload/nipt/models.py:7: unused variable 'multiqc_report' (60% confidence)
cg/meta/upload/nipt/models.py:8: unused variable 'segmental_calls' (60% confidence) cg/models/balsamic/config.py:23: unused variable 'analysis_workflow' (60% confidence)
cg/models/balsamic/config.py:25: unused variable 'BALSAMIC_version' (60% confidence)
cg/models/balsamic/config.py:26: unused variable 'config_creation_date' (60% confidence)
cg/models/balsamic/config.py:54: unused variable 'reference_access_date' (60% confidence) cg/models/balsamic/config.py:83: unused variable 'chrom' (60% confidence) cg/models/balsamic/config.py:108: unused variable 'picard_rmdup' (60% confidence)
cg/models/balsamic/config.py:109: unused variable 'adapter' (60% confidence)
cg/models/balsamic/config.py:110: unused variable 'quality_trim' (60% confidence)
cg/models/balsamic/config.py:111: unused variable 'adapter_trim' (60% confidence)
cg/models/balsamic/config.py:112: unused variable 'umi_trim' (60% confidence)
cg/models/balsamic/config.py:113: unused variable 'min_seq_length' (60% confidence)
cg/models/balsamic/config.py:114: unused variable 'umi_trim_length' (60% confidence)
cg/models/balsamic/config.py:128: unused variable 'mutation' (60% confidence)
cg/models/balsamic/config.py:132: unused variable 'workflow_solution' (60% confidence)
cg/models/balsamic/metrics.py:22: unused variable 'norm' (60% confidence)
cg/models/balsamic/metrics.py:33: unused variable 'condition' (60% confidence)
cg/models/balsamic/metrics.py:46: unused variable 'mean_target_coverage' (60% confidence)
cg/models/balsamic/metrics.py:49: unused variable 'pct_target_bases_50x' (60% confidence)
cg/models/balsamic/metrics.py:50: unused variable 'pct_target_bases_100x' (60% confidence)
cg/models/balsamic/metrics.py:53: unused variable 'pct_target_bases_1000x' (60% confidence)
cg/models/balsamic/metrics.py:54: unused variable 'pct_off_bait' (60% confidence)
cg/models/balsamic/metrics.py:75: unused variable 'pct_30x' (60% confidence)
cg/models/balsamic/metrics.py:77: unused variable 'pct_100x' (60% confidence)
cg/models/cg_config.py:30: unused variable 'hiseqx' (60% confidence)
cg/models/cg_config.py:31: unused variable 'hiseqga' (60% confidence)
cg/models/cg_config.py:32: unused variable 'novaseq' (60% confidence)
cg/models/cg_config.py:36: unused variable 'current' (60% confidence)
cg/models/cg_config.py:37: unused variable 'legacy' (60% confidence)
cg/models/cg_config.py:120: unused variable 'cram_reference' (60% confidence)
cg/models/cg_config.py:125: unused variable 'padding' (60% confidence)
cg/models/cg_config.py:195: unused variable 'covid_source_path' (60% confidence)
cg/models/cg_config.py:235: unused variable 'madeline_exe' (60% confidence)
cg/models/cg_config.py:237: unused variable 'max_flowcells' (60% confidence)
cg/models/cg_config.py:241: unused variable 'status_db_' (60% confidence)
cg/models/cg_config.py:243: unused variable 'housekeeper_api_' (60% confidence)
cg/models/cg_config.py:247: unused variable 'cgstats' (60% confidence)
cg/models/cg_config.py:248: unused variable 'cg_stats_api_' (60% confidence)
cg/models/cg_config.py:249: unused variable 'chanjo' (60% confidence)
cg/models/cg_config.py:250: unused variable 'chanjo_api_' (60% confidence)
cg/models/cg_config.py:252: unused variable 'crunchy' (60% confidence)
cg/models/cg_config.py:253: unused variable 'crunchy_api_' (60% confidence)
cg/models/cg_config.py:255: unused variable 'ddn' (60% confidence)
cg/models/cg_config.py:257: unused variable 'demultiplex_api_' (60% confidence)
cg/models/cg_config.py:260: unused variable 'genotype' (60% confidence)
cg/models/cg_config.py:261: unused variable 'genotype_api_' (60% confidence)
cg/models/cg_config.py:263: unused variable 'gens_api_' (60% confidence)
cg/models/cg_config.py:264: unused variable 'hermes' (60% confidence)
cg/models/cg_config.py:265: unused variable 'hermes_api_' (60% confidence)
cg/models/cg_config.py:267: unused variable 'lims_api_' (60% confidence)
cg/models/cg_config.py:269: unused variable 'loqusdb_api_' (60% confidence)
cg/models/cg_config.py:273: unused variable 'madeline_api_' (60% confidence)
cg/models/cg_config.py:275: unused variable 'mutacc_auto_api_' (60% confidence)
cg/models/cg_config.py:278: unused variable 'scout_api_' (60% confidence)
cg/models/cg_config.py:280: unused variable 'trailblazer' (60% confidence)
cg/models/cg_config.py:281: unused variable 'trailblazer_api_' (60% confidence)
cg/models/cg_config.py:283: unused variable 'vogue_api_' (60% confidence) cg/models/cg_config.py:301: unused variable 'arbitrary_types_allowed' (60% confidence) cg/models/cgstats/stats_sample.py:10: unused variable 'passed_filter_pct' (60% confidence) cg/models/cgstats/stats_sample.py:56: unused variable 'orm_mode' (60% confidence) cg/models/deliverables/metric_deliverables.py:90: unused variable 'median_target_coverage_step' (60% confidence) cg/models/demultiplex/sbatch.py:10: unused variable 'demux_started' (60% confidence)
cg/models/demultiplex/sbatch.py:18: unused variable 'demux_completed_file' (60% confidence)
cg/models/invoice/invoice.py:15: unused variable 'address' (60% confidence)
cg/models/invoice/invoice.py:46: unused variable 'project_number' (60% confidence)
cg/models/invoice/invoice.py:49: unused variable 'agreement' (60% confidence)
cg/models/lims/sample.py:14: unused variable 'collection_date' (60% confidence)
cg/models/lims/sample.py:16: unused variable 'concentration' (60% confidence)
cg/models/lims/sample.py:17: unused variable 'concentration_sample' (60% confidence)
cg/models/lims/sample.py:22: unused variable 'elution_buffer' (60% confidence)
cg/models/lims/sample.py:23: unused variable 'extraction_method' (60% confidence)
cg/models/lims/sample.py:25: unused variable 'formalin_fixation_time' (60% confidence)
cg/models/lims/sample.py:27: unused variable 'index_number' (60% confidence)
cg/models/lims/sample.py:30: unused variable 'organism_other' (60% confidence)
cg/models/lims/sample.py:31: unused variable 'original_lab' (60% confidence)
cg/models/lims/sample.py:32: unused variable 'original_lab_address' (60% confidence)
cg/models/lims/sample.py:34: unused variable 'post_formalin_fixation_time' (60% confidence)
cg/models/lims/sample.py:35: unused variable 'pre_processing_method' (60% confidence)
cg/models/lims/sample.py:36: unused variable 'primer' (60% confidence)
cg/models/lims/sample.py:38: unused variable 'quantity' (60% confidence)
cg/models/lims/sample.py:42: unused variable 'require_qcok' (60% confidence)
cg/models/lims/sample.py:43: unused variable 'rml_plate_name' (60% confidence)
cg/models/lims/sample.py:44: unused variable 'selection_criteria' (60% confidence)
cg/models/lims/sample.py:47: unused variable 'tissue_block_size' (60% confidence)
cg/models/lims/sample.py:49: unused variable 'tumour_purity' (60% confidence)
cg/models/lims/sample.py:51: unused variable 'well_position_rml' (60% confidence)
cg/models/lims/sample.py:52: unused variable 'verified_organism' (60% confidence) cg/models/lims/sample.py:63: unused variable 'well_position' (60% confidence)
cg/models/mip/mip_config.py:17: unused variable 'family_id_' (60% confidence)
cg/models/mip/mip_config.py:19: unused variable 'analysis_type_' (60% confidence)
cg/models/mip/mip_config.py:24: unused variable 'is_dry_run' (60% confidence)
cg/models/mip/mip_config.py:28: unused variable 'sample_info_path' (60% confidence) cg/models/mip/mip_metrics_deliverables.py:57: unused variable 'duplicate_reads_step' (60% confidence)
cg/models/mip/mip_metrics_deliverables.py:59: unused variable 'mapped_reads_step' (60% confidence)
cg/models/mip/mip_metrics_deliverables.py:61: unused variable 'predicted_sex_step' (60% confidence)
cg/models/mip/mip_metrics_deliverables.py:67: unused variable 'metric_to_get_' (60% confidence)
cg/models/mip/mip_metrics_deliverables.py:78: unused variable 'sample_metric_to_parse' (60% confidence) cg/models/mip/mip_sample_info.py:12: unused variable 'family_id_' (60% confidence)
cg/models/mip/mip_sample_info.py:14: unused variable 'human_genome_build_' (60% confidence)
cg/models/mip/mip_sample_info.py:16: unused variable 'program_' (60% confidence)
cg/models/mip/mip_sample_info.py:17: unused variable 'recipe_' (60% confidence)
cg/models/mip/mip_sample_info.py:20: unused variable 'analysis_run_status_' (60% confidence)
cg/models/mip/mip_sample_info.py:22: unused variable 'is_finished' (60% confidence) cg/models/orders/excel_sample.py:13: unused variable 'collection_date' (60% confidence)
cg/models/orders/excel_sample.py:15: unused variable 'concentration' (60% confidence)
cg/models/orders/excel_sample.py:16: unused variable 'concentration_sample' (60% confidence)
cg/models/orders/excel_sample.py:20: unused variable 'custom_index' (60% confidence)
cg/models/orders/excel_sample.py:24: unused variable 'elution_buffer' (60% confidence)
cg/models/orders/excel_sample.py:25: unused variable 'extraction_method' (60% confidence)
cg/models/orders/excel_sample.py:28: unused variable 'formalin_fixation_time' (60% confidence)
cg/models/orders/excel_sample.py:30: unused variable 'index_number' (60% confidence)
cg/models/orders/excel_sample.py:35: unused variable 'organism_other' (60% confidence)
cg/models/orders/excel_sample.py:36: unused variable 'original_lab' (60% confidence)
cg/models/orders/excel_sample.py:37: unused variable 'original_lab_address' (60% confidence)
cg/models/orders/excel_sample.py:40: unused variable 'post_formalin_fixation_time' (60% confidence)
cg/models/orders/excel_sample.py:41: unused variable 'pre_processing_method' (60% confidence)
cg/models/orders/excel_sample.py:42: unused variable 'primer' (60% confidence)
cg/models/orders/excel_sample.py:44: unused variable 'quantity' (60% confidence)
cg/models/orders/excel_sample.py:49: unused variable 'require_qcok' (60% confidence)
cg/models/orders/excel_sample.py:50: unused variable 'rml_plate_name' (60% confidence)
cg/models/orders/excel_sample.py:51: unused variable 'selection_criteria' (60% confidence)
cg/models/orders/excel_sample.py:57: unused variable 'tissue_block_size' (60% confidence)
cg/models/orders/excel_sample.py:59: unused variable 'tumour_purity' (60% confidence)
cg/models/orders/excel_sample.py:61: unused variable 'well_position' (60% confidence)
cg/models/orders/excel_sample.py:62: unused variable 'well_position_rml' (60% confidence) cg/models/orders/json_sample.py:10: unused variable 'concentration' (60% confidence)
cg/models/orders/json_sample.py:11: unused variable 'concentration_sample' (60% confidence)
cg/models/orders/json_sample.py:17: unused variable 'quantity' (60% confidence)
cg/models/orders/json_sample.py:19: unused variable 'well_position' (60% confidence) cg/models/orders/sample_base.py:11: unused variable 'not_control' (60% confidence)
cg/models/orders/sample_base.py:12: unused variable 'positive' (60% confidence)
cg/models/orders/sample_base.py:17: unused variable 'male' (60% confidence)
cg/models/orders/sample_base.py:18: unused variable 'female' (60% confidence)
cg/models/orders/sample_base.py:32: unused variable 'plate' (60% confidence)
cg/models/orders/sample_base.py:33: unused variable 'tube' (60% confidence)
cg/models/orders/sample_base.py:37: unused variable 'affected' (60% confidence)
cg/models/orders/sample_base.py:38: unused variable 'unaffected' (60% confidence)
cg/models/orders/sample_base.py:49: unused variable 'collection_date' (60% confidence)
cg/models/orders/sample_base.py:51: unused variable 'concentration' (60% confidence)
cg/models/orders/sample_base.py:52: unused variable 'concentration_sample' (60% confidence)
cg/models/orders/sample_base.py:57: unused variable 'custom_index' (60% confidence)
cg/models/orders/sample_base.py:60: unused variable 'elution_buffer' (60% confidence)
cg/models/orders/sample_base.py:61: unused variable 'extraction_method' (60% confidence)
cg/models/orders/sample_base.py:72: unused variable 'formalin_fixation_time' (60% confidence)
cg/models/orders/sample_base.py:74: unused variable 'index_number' (60% confidence)
cg/models/orders/sample_base.py:87: unused variable 'organism_other' (60% confidence)
cg/models/orders/sample_base.py:88: unused variable 'original_lab' (60% confidence)
cg/models/orders/sample_base.py:89: unused variable 'original_lab_address' (60% confidence)
cg/models/orders/sample_base.py:93: unused variable 'post_formalin_fixation_time' (60% confidence)
cg/models/orders/sample_base.py:94: unused variable 'pre_processing_method' (60% confidence)
cg/models/orders/sample_base.py:96: unused variable 'quantity' (60% confidence)
cg/models/orders/sample_base.py:103: unused variable 'require_qcok' (60% confidence)
cg/models/orders/sample_base.py:104: unused variable 'rml_plate_name' (60% confidence)
cg/models/orders/sample_base.py:105: unused variable 'selection_criteria' (60% confidence)
cg/models/orders/sample_base.py:112: unused variable 'tissue_block_size' (60% confidence)
cg/models/orders/sample_base.py:114: unused variable 'tumour_purity' (60% confidence)
cg/models/orders/sample_base.py:115: unused variable 'verified_organism' (60% confidence)
cg/models/orders/sample_base.py:117: unused variable 'well_position' (60% confidence)
cg/models/orders/sample_base.py:118: unused variable 'well_position_rml' (60% confidence) cg/models/orders/samples.py:47: unused variable 'require_qcok' (60% confidence)
cg/models/orders/samples.py:86: unused variable 'well_position' (60% confidence)
cg/models/orders/samples.py:97: unused variable 'elution_buffer' (60% confidence)
cg/models/orders/samples.py:98: unused variable 'tumour_purity' (60% confidence)
cg/models/orders/samples.py:100: unused variable 'formalin_fixation_time' (60% confidence)
cg/models/orders/samples.py:101: unused variable 'post_formalin_fixation_time' (60% confidence)
cg/models/orders/samples.py:102: unused variable 'tissue_block_size' (60% confidence)
cg/models/orders/samples.py:107: unused variable 'require_qcok' (60% confidence) cg/models/orders/samples.py:174: unused variable 'well_position' (60% confidence)
cg/models/orders/samples.py:175: unused variable 'elution_buffer' (60% confidence)
cg/models/orders/samples.py:179: unused variable 'quantity' (60% confidence)
cg/models/orders/samples.py:193: unused variable 'concentration' (60% confidence)
cg/models/orders/samples.py:194: unused variable 'concentration_sample' (60% confidence)
cg/models/orders/samples.py:196: unused variable 'index_number' (60% confidence)
cg/models/orders/samples.py:198: unused variable 'rml_plate_name' (60% confidence)
cg/models/orders/samples.py:199: unused variable 'well_position_rml' (60% confidence) cg/models/orders/samples.py:221: unused variable 'elution_buffer' (60% confidence)
cg/models/orders/samples.py:225: unused variable 'well_position' (60% confidence)
cg/models/orders/samples.py:227: unused variable 'concentration_sample' (60% confidence)
cg/models/orders/samples.py:228: unused variable 'quantity' (60% confidence)
cg/models/orders/samples.py:229: unused variable 'extraction_method' (60% confidence)
cg/models/orders/samples.py:246: unused variable 'elution_buffer' (60% confidence)
cg/models/orders/samples.py:247: unused variable 'extraction_method' (60% confidence)
cg/models/orders/samples.py:251: unused variable 'well_position' (60% confidence)
cg/models/orders/samples.py:253: unused variable 'organism_other' (60% confidence)
cg/models/orders/samples.py:257: unused variable 'concentration_sample' (60% confidence)
cg/models/orders/samples.py:258: unused variable 'quantity' (60% confidence)
cg/models/orders/samples.py:259: unused variable 'verified_organism' (60% confidence) cg/models/orders/samples.py:281: unused variable 'collection_date' (60% confidence)
cg/models/orders/samples.py:283: unused variable 'primer' (60% confidence)
cg/models/orders/samples.py:284: unused variable 'original_lab' (60% confidence)
cg/models/orders/samples.py:285: unused variable 'original_lab_address' (60% confidence)
cg/models/orders/samples.py:286: unused variable 'pre_processing_method' (60% confidence)
cg/models/orders/samples.py:289: unused variable 'selection_criteria' (60% confidence)
cg/models/report/metadata.py:18: unused variable 'duplicates' (60% confidence)
cg/models/report/metadata.py:36: unused variable 'bait_set' (60% confidence)
cg/models/report/metadata.py:39: unused variable 'mean_target_coverage' (60% confidence)
cg/models/report/metadata.py:40: unused variable 'pct_10x' (60% confidence)
cg/models/report/metadata.py:59: unused variable 'fold_80' (60% confidence)
cg/models/report/metadata.py:77: unused variable 'bait_set' (60% confidence)
cg/models/report/metadata.py:78: unused variable 'bait_set_version' (60% confidence)
cg/models/report/metadata.py:80: unused variable 'pct_250x' (60% confidence)
cg/models/report/metadata.py:81: unused variable 'pct_500x' (60% confidence)
cg/models/report/report.py:50: unused variable 'snv_vcf' (60% confidence)
cg/models/report/report.py:51: unused variable 'snv_research_vcf' (60% confidence)
cg/models/report/report.py:52: unused variable 'sv_vcf' (60% confidence)
cg/models/report/report.py:53: unused variable 'sv_research_vcf' (60% confidence)
cg/models/report/report.py:54: unused variable 'vcf_str' (60% confidence)
cg/models/report/report.py:55: unused variable 'smn_tsv' (60% confidence)
cg/models/report/report.py:85: unused variable 'customer_pipeline' (60% confidence)
cg/models/report/report.py:91: unused variable 'variant_callers' (60% confidence)
cg/models/report/report.py:93: unused variable 'scout_files' (60% confidence) cg/models/scout/scout_load_config.py:11: unused variable 'autozygous' (60% confidence)
cg/models/scout/scout_load_config.py:13: unused variable 'upd_regions' (60% confidence)
cg/models/scout/scout_load_config.py:14: unused variable 'upd_sites' (60% confidence)
cg/models/scout/scout_load_config.py:18: unused variable 'alignment' (60% confidence)
cg/models/scout/scout_load_config.py:19: unused variable 'alignment_index' (60% confidence)
cg/models/scout/scout_load_config.py:21: unused variable 'catalog' (60% confidence)
cg/models/scout/scout_load_config.py:37: unused variable 'confirmed_parent' (60% confidence)
cg/models/scout/scout_load_config.py:38: unused variable 'confirmed_sex' (60% confidence) cg/models/scout/scout_load_config.py:55: unused variable 'validate_assignment' (60% confidence)
cg/models/scout/scout_load_config.py:59: unused variable 'mt_bam' (60% confidence)
cg/models/scout/scout_load_config.py:60: unused variable 'chromograph_images' (60% confidence)
cg/models/scout/scout_load_config.py:61: unused variable 'reviewer' (60% confidence)
cg/models/scout/scout_load_config.py:62: unused variable 'rhocall_bed' (60% confidence)
cg/models/scout/scout_load_config.py:63: unused variable 'rhocall_wig' (60% confidence)
cg/models/scout/scout_load_config.py:64: unused variable 'tiddit_coverage_wig' (60% confidence)
cg/models/scout/scout_load_config.py:65: unused variable 'upd_regions_bed' (60% confidence)
cg/models/scout/scout_load_config.py:66: unused variable 'upd_sites_bed' (60% confidence)
cg/models/scout/scout_load_config.py:67: unused variable 'vcf2cytosure' (60% confidence)
cg/models/scout/scout_load_config.py:68: unused variable 'mitodel_file' (60% confidence)
cg/models/scout/scout_load_config.py:72: unused variable 'tumor_type' (60% confidence)
cg/models/scout/scout_load_config.py:73: unused variable 'tmb' (60% confidence)
cg/models/scout/scout_load_config.py:74: unused variable 'msi' (60% confidence)
cg/models/scout/scout_load_config.py:75: unused variable 'tumor_purity' (60% confidence)
cg/models/scout/scout_load_config.py:76: unused variable 'vcf2cytosure' (60% confidence)
cg/models/scout/scout_load_config.py:86: unused variable 'gene_panels' (60% confidence)
cg/models/scout/scout_load_config.py:87: unused variable 'default_gene_panels' (60% confidence)
cg/models/scout/scout_load_config.py:89: unused variable 'human_genome_build' (60% confidence)
cg/models/scout/scout_load_config.py:92: unused variable 'rank_score_threshold' (60% confidence)
cg/models/scout/scout_load_config.py:98: unused variable 'coverage_qc_report' (60% confidence)
cg/models/scout/scout_load_config.py:99: unused variable 'cnv_report' (60% confidence)
cg/models/scout/scout_load_config.py:100: unused variable 'multiqc' (60% confidence) cg/models/scout/scout_load_config.py:110: unused variable 'validate_assignment' (60% confidence)
cg/models/scout/scout_load_config.py:114: unused variable 'madeline' (60% confidence)
cg/models/scout/scout_load_config.py:115: unused variable 'vcf_cancer' (60% confidence)
cg/models/scout/scout_load_config.py:116: unused variable 'vcf_cancer_sv' (60% confidence)
cg/models/scout/scout_load_config.py:117: unused variable 'vcf_cancer_research' (60% confidence) cg/models/scout/scout_load_config.py:133: unused variable 'smn_tsv' (60% confidence)
cg/models/scout/scout_load_config.py:134: unused variable 'chromograph_image_files' (60% confidence)
cg/models/scout/scout_load_config.py:135: unused variable 'chromograph_prefixes' (60% confidence)
cg/models/scout/scout_load_config.py:136: unused variable 'vcf_snv' (60% confidence)
cg/models/scout/scout_load_config.py:137: unused variable 'vcf_sv' (60% confidence)
cg/models/scout/scout_load_config.py:138: unused variable 'vcf_str' (60% confidence)
cg/models/scout/scout_load_config.py:139: unused variable 'vcf_snv_research' (60% confidence)
cg/models/scout/scout_load_config.py:140: unused variable 'vcf_sv_research' (60% confidence)
cg/models/scout/scout_load_config.py:141: unused variable 'peddy_ped' (60% confidence)
cg/models/scout/scout_load_config.py:142: unused variable 'peddy_sex' (60% confidence)
cg/models/scout/scout_load_config.py:143: unused variable 'peddy_check' (60% confidence)
cg/models/scout/scout_load_config.py:144: unused variable 'madeline' (60% confidence) cg/models/scout/scout_load_config.py:156: unused variable 'multiqc_rna' (60% confidence)
cg/models/scout/scout_load_config.py:157: unused variable 'gene_fusion' (60% confidence)
cg/models/scout/scout_load_config.py:158: unused variable 'gene_fusion_research' (60% confidence)
cg/models/scout/scout_load_config.py:159: unused variable 'RNAfusion_inspector' (60% confidence)
cg/models/scout/scout_load_config.py:160: unused variable 'RNAfusion_inspector_research' (60% confidence)
cg/models/scout/scout_load_config.py:161: unused variable 'RNAfusion_report' (60% confidence)
cg/models/scout/scout_load_config.py:162: unused variable 'RNAfusion_report_research' (60% confidence)
cg/models/slurm/sbatch.py:10: unused variable 'use_login_shell' (60% confidence)
cg/models/slurm/sbatch.py:11: unused variable 'job_name' (60% confidence)
cg/models/slurm/sbatch.py:16: unused variable 'minutes' (60% confidence)
cg/models/slurm/sbatch.py:17: unused variable 'quality_of_service' (60% confidence)
cg/models/slurm/sbatch.py:20: unused variable 'exclude' (60% confidence)
cg/models/slurm/sbatch.py:26: unused variable 'partition' (60% confidence)
cg/models/slurm/sbatch.py:27: unused variable 'nodes' (60% confidence)
cg/models/slurm/sbatch.py:28: unused variable 'cpus_per_task' (60% confidence)
cg/models/workflow/mutant.py:5: unused variable 'CG_ID_project' (60% confidence)
cg/models/workflow/mutant.py:6: unused variable 'CG_ID_sample' (60% confidence)
cg/models/workflow/mutant.py:7: unused variable 'case_ID' (60% confidence)
cg/models/workflow/mutant.py:11: unused variable 'Customer_ID_project' (60% confidence)
cg/models/workflow/mutant.py:12: unused variable 'Customer_ID_sample' (60% confidence)
cg/models/workflow/mutant.py:15: unused variable 'date_arrival' (60% confidence)
cg/models/workflow/mutant.py:16: unused variable 'date_libprep' (60% confidence)
cg/models/workflow/mutant.py:17: unused variable 'date_sequencing' (60% confidence)
cg/models/workflow/mutant.py:18: unused variable 'method_libprep' (60% confidence)
cg/models/workflow/mutant.py:20: unused variable 'sequencing_qc_pass' (60% confidence)
cg/models/workflow/mutant.py:21: unused variable 'selection_criteria' (60% confidence) cg/store/models.py:99: unused variable 'minimum_order' (60% confidence)
cg/store/models.py:100: unused variable 'sequencing_depth' (60% confidence)
cg/store/models.py:104: unused variable 'sample_amount' (60% confidence)
cg/store/models.py:105: unused variable 'sample_volume' (60% confidence)
cg/store/models.py:106: unused variable 'sample_concentration' (60% confidence)
cg/store/models.py:107: unused variable 'priority_processing' (60% confidence)
cg/store/models.py:108: unused variable 'details' (60% confidence) cg/store/models.py:154: unused variable 'price_standard' (60% confidence)
cg/store/models.py:155: unused variable 'price_priority' (60% confidence)
cg/store/models.py:156: unused variable 'price_express' (60% confidence)
cg/store/models.py:157: unused variable 'price_research' (60% confidence)
cg/store/models.py:158: unused variable 'price_clinical_trials' (60% confidence)
cg/store/models.py:189: unused variable 'is_primary' (60% confidence)
cg/store/models.py:234: unused variable 'panel_size' (60% confidence)
cg/store/models.py:236: unused variable 'designer' (60% confidence)
cg/store/models.py:240: unused variable 'bed_id' (60% confidence)
cg/store/models.py:255: unused variable 'agreement_date' (60% confidence)
cg/store/models.py:264: unused variable 'organisation_number' (60% confidence)
cg/store/models.py:266: unused variable 'project_account_ki' (60% confidence)
cg/store/models.py:267: unused variable 'project_account_kth' (60% confidence)
cg/store/models.py:268: unused variable 'return_samples' (60% confidence)
cg/store/models.py:270: unused variable 'uppmax_account' (60% confidence)
cg/store/models.py:274: unused variable 'delivery_contact' (60% confidence)
cg/store/models.py:278: unused variable 'primary_contact' (60% confidence)
cg/store/models.py:322: unused variable 'removed_at' (60% confidence)
cg/store/models.py:548: unused variable 'gene_count' (60% confidence)
cg/store/models.py:569: unused variable 'deliveries' (60% confidence)
cg/store/models.py:594: unused variable 'deliveries' (60% confidence)
seallard commented 1 year ago

Too vague