cg 83.18.0__tar.gz → 83.18.1__tar.gz

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.
Files changed (928) hide show
  1. {cg-83.18.0 → cg-83.18.1}/PKG-INFO +1 -1
  2. cg-83.18.1/cg/__init__.py +2 -0
  3. {cg-83.18.0 → cg-83.18.1}/cg/constants/nf_analysis.py +2 -0
  4. {cg-83.18.0 → cg-83.18.1}/pyproject.toml +1 -1
  5. cg-83.18.0/cg/__init__.py +0 -2
  6. {cg-83.18.0 → cg-83.18.1}/README.md +0 -0
  7. {cg-83.18.0 → cg-83.18.1}/cg/apps/__init__.py +0 -0
  8. {cg-83.18.0 → cg-83.18.1}/cg/apps/coverage/__init__.py +0 -0
  9. {cg-83.18.0 → cg-83.18.1}/cg/apps/coverage/api.py +0 -0
  10. {cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/__init__.py +0 -0
  11. {cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/crunchy.py +0 -0
  12. {cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/files.py +0 -0
  13. {cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/models.py +0 -0
  14. {cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/sbatch.py +0 -0
  15. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/__init__.py +0 -0
  16. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/demultiplex_api.py +0 -0
  17. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/__init__.py +0 -0
  18. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/api.py +0 -0
  19. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/index.py +0 -0
  20. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/override_cycles_validator.py +0 -0
  21. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/read_sample_sheet.py +0 -0
  22. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/sample_models.py +0 -0
  23. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/sample_sheet_creator.py +0 -0
  24. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/sample_sheet_models.py +0 -0
  25. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/sample_sheet_validator.py +0 -0
  26. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/utils.py +0 -0
  27. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sample_sheet/validators.py +0 -0
  28. {cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sbatch.py +0 -0
  29. {cg-83.18.0 → cg-83.18.1}/cg/apps/downsample/__init__.py +0 -0
  30. {cg-83.18.0 → cg-83.18.1}/cg/apps/downsample/downsample.py +0 -0
  31. {cg-83.18.0 → cg-83.18.1}/cg/apps/downsample/utils.py +0 -0
  32. {cg-83.18.0 → cg-83.18.1}/cg/apps/environ.py +0 -0
  33. {cg-83.18.0 → cg-83.18.1}/cg/apps/gens.py +0 -0
  34. {cg-83.18.0 → cg-83.18.1}/cg/apps/gt.py +0 -0
  35. {cg-83.18.0 → cg-83.18.1}/cg/apps/hermes/__init__.py +0 -0
  36. {cg-83.18.0 → cg-83.18.1}/cg/apps/hermes/hermes_api.py +0 -0
  37. {cg-83.18.0 → cg-83.18.1}/cg/apps/hermes/models.py +0 -0
  38. {cg-83.18.0 → cg-83.18.1}/cg/apps/housekeeper/__init__.py +0 -0
  39. {cg-83.18.0 → cg-83.18.1}/cg/apps/housekeeper/hk.py +0 -0
  40. {cg-83.18.0 → cg-83.18.1}/cg/apps/housekeeper/models.py +0 -0
  41. {cg-83.18.0 → cg-83.18.1}/cg/apps/invoice/__init__.py +0 -0
  42. {cg-83.18.0 → cg-83.18.1}/cg/apps/invoice/render.py +0 -0
  43. {cg-83.18.0 → cg-83.18.1}/cg/apps/invoice/templates/KI_pool_invoice.xlsx +0 -0
  44. {cg-83.18.0 → cg-83.18.1}/cg/apps/invoice/templates/KI_sample_invoice.xlsx +0 -0
  45. {cg-83.18.0 → cg-83.18.1}/cg/apps/invoice/templates/KTH_pool_invoice.xlsx +0 -0
  46. {cg-83.18.0 → cg-83.18.1}/cg/apps/invoice/templates/KTH_sample_invoice.xlsx +0 -0
  47. {cg-83.18.0 → cg-83.18.1}/cg/apps/lims/__init__.py +0 -0
  48. {cg-83.18.0 → cg-83.18.1}/cg/apps/lims/api.py +0 -0
  49. {cg-83.18.0 → cg-83.18.1}/cg/apps/lims/batch.py +0 -0
  50. {cg-83.18.0 → cg-83.18.1}/cg/apps/lims/order.py +0 -0
  51. {cg-83.18.0 → cg-83.18.1}/cg/apps/lims/sample_sheet.py +0 -0
  52. {cg-83.18.0 → cg-83.18.1}/cg/apps/loqus.py +0 -0
  53. {cg-83.18.0 → cg-83.18.1}/cg/apps/madeline/__init__.py +0 -0
  54. {cg-83.18.0 → cg-83.18.1}/cg/apps/madeline/api.py +0 -0
  55. {cg-83.18.0 → cg-83.18.1}/cg/apps/mip/__init__.py +0 -0
  56. {cg-83.18.0 → cg-83.18.1}/cg/apps/mip/confighandler.py +0 -0
  57. {cg-83.18.0 → cg-83.18.1}/cg/apps/mutacc_auto.py +0 -0
  58. {cg-83.18.0 → cg-83.18.1}/cg/apps/orderform/__init__.py +0 -0
  59. {cg-83.18.0 → cg-83.18.1}/cg/apps/orderform/excel_orderform_parser.py +0 -0
  60. {cg-83.18.0 → cg-83.18.1}/cg/apps/orderform/json_orderform_parser.py +0 -0
  61. {cg-83.18.0 → cg-83.18.1}/cg/apps/orderform/orderform_parser.py +0 -0
  62. {cg-83.18.0 → cg-83.18.1}/cg/apps/orderform/utils.py +0 -0
  63. {cg-83.18.0 → cg-83.18.1}/cg/apps/scout/__init__.py +0 -0
  64. {cg-83.18.0 → cg-83.18.1}/cg/apps/scout/scout_export.py +0 -0
  65. {cg-83.18.0 → cg-83.18.1}/cg/apps/scout/scoutapi.py +0 -0
  66. {cg-83.18.0 → cg-83.18.1}/cg/apps/scout/validators.py +0 -0
  67. {cg-83.18.0 → cg-83.18.1}/cg/apps/slurm/__init__.py +0 -0
  68. {cg-83.18.0 → cg-83.18.1}/cg/apps/slurm/sbatch.py +0 -0
  69. {cg-83.18.0 → cg-83.18.1}/cg/apps/slurm/slurm_api.py +0 -0
  70. {cg-83.18.0 → cg-83.18.1}/cg/apps/tb/__init__.py +0 -0
  71. {cg-83.18.0 → cg-83.18.1}/cg/apps/tb/api.py +0 -0
  72. {cg-83.18.0 → cg-83.18.1}/cg/apps/tb/dto/create_job_request.py +0 -0
  73. {cg-83.18.0 → cg-83.18.1}/cg/apps/tb/dto/summary_response.py +0 -0
  74. {cg-83.18.0 → cg-83.18.1}/cg/apps/tb/models.py +0 -0
  75. {cg-83.18.0 → cg-83.18.1}/cg/apps/tb/validators.py +0 -0
  76. {cg-83.18.0 → cg-83.18.1}/cg/cli/__init__.py +0 -0
  77. {cg-83.18.0 → cg-83.18.1}/cg/cli/add.py +0 -0
  78. {cg-83.18.0 → cg-83.18.1}/cg/cli/archive.py +0 -0
  79. {cg-83.18.0 → cg-83.18.1}/cg/cli/backup.py +0 -0
  80. {cg-83.18.0 → cg-83.18.1}/cg/cli/base.py +0 -0
  81. {cg-83.18.0 → cg-83.18.1}/cg/cli/clean.py +0 -0
  82. {cg-83.18.0 → cg-83.18.1}/cg/cli/compress/__init__.py +0 -0
  83. {cg-83.18.0 → cg-83.18.1}/cg/cli/compress/base.py +0 -0
  84. {cg-83.18.0 → cg-83.18.1}/cg/cli/compress/fastq.py +0 -0
  85. {cg-83.18.0 → cg-83.18.1}/cg/cli/compress/helpers.py +0 -0
  86. {cg-83.18.0 → cg-83.18.1}/cg/cli/delete/__init__.py +0 -0
  87. {cg-83.18.0 → cg-83.18.1}/cg/cli/delete/base.py +0 -0
  88. {cg-83.18.0 → cg-83.18.1}/cg/cli/delete/case.py +0 -0
  89. {cg-83.18.0 → cg-83.18.1}/cg/cli/delete/cases.py +0 -0
  90. {cg-83.18.0 → cg-83.18.1}/cg/cli/delete/illumina_sequencing_run.py +0 -0
  91. {cg-83.18.0 → cg-83.18.1}/cg/cli/delete/observations.py +0 -0
  92. {cg-83.18.0 → cg-83.18.1}/cg/cli/deliver/__init__.py +0 -0
  93. {cg-83.18.0 → cg-83.18.1}/cg/cli/deliver/base.py +0 -0
  94. {cg-83.18.0 → cg-83.18.1}/cg/cli/deliver/utils.py +0 -0
  95. {cg-83.18.0 → cg-83.18.1}/cg/cli/demultiplex/__init__.py +0 -0
  96. {cg-83.18.0 → cg-83.18.1}/cg/cli/demultiplex/base.py +0 -0
  97. {cg-83.18.0 → cg-83.18.1}/cg/cli/demultiplex/copy_novaseqx_demultiplex_data.py +0 -0
  98. {cg-83.18.0 → cg-83.18.1}/cg/cli/demultiplex/demux.py +0 -0
  99. {cg-83.18.0 → cg-83.18.1}/cg/cli/demultiplex/finish.py +0 -0
  100. {cg-83.18.0 → cg-83.18.1}/cg/cli/demultiplex/sample_sheet.py +0 -0
  101. {cg-83.18.0 → cg-83.18.1}/cg/cli/downsample.py +0 -0
  102. {cg-83.18.0 → cg-83.18.1}/cg/cli/generate/__init__.py +0 -0
  103. {cg-83.18.0 → cg-83.18.1}/cg/cli/generate/base.py +0 -0
  104. {cg-83.18.0 → cg-83.18.1}/cg/cli/generate/delivery_report/__init__.py +0 -0
  105. {cg-83.18.0 → cg-83.18.1}/cg/cli/generate/delivery_report/base.py +0 -0
  106. {cg-83.18.0 → cg-83.18.1}/cg/cli/generate/delivery_report/options.py +0 -0
  107. {cg-83.18.0 → cg-83.18.1}/cg/cli/generate/delivery_report/utils.py +0 -0
  108. {cg-83.18.0 → cg-83.18.1}/cg/cli/get.py +0 -0
  109. {cg-83.18.0 → cg-83.18.1}/cg/cli/post_process/__init__.py +0 -0
  110. {cg-83.18.0 → cg-83.18.1}/cg/cli/post_process/post_process.py +0 -0
  111. {cg-83.18.0 → cg-83.18.1}/cg/cli/post_process/utils.py +0 -0
  112. {cg-83.18.0 → cg-83.18.1}/cg/cli/sequencing_qc/sequencing_qc.py +0 -0
  113. {cg-83.18.0 → cg-83.18.1}/cg/cli/set/__init__.py +0 -0
  114. {cg-83.18.0 → cg-83.18.1}/cg/cli/set/base.py +0 -0
  115. {cg-83.18.0 → cg-83.18.1}/cg/cli/set/case.py +0 -0
  116. {cg-83.18.0 → cg-83.18.1}/cg/cli/set/cases.py +0 -0
  117. {cg-83.18.0 → cg-83.18.1}/cg/cli/store/__init__.py +0 -0
  118. {cg-83.18.0 → cg-83.18.1}/cg/cli/store/base.py +0 -0
  119. {cg-83.18.0 → cg-83.18.1}/cg/cli/store/store.py +0 -0
  120. {cg-83.18.0 → cg-83.18.1}/cg/cli/transfer.py +0 -0
  121. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/__init__.py +0 -0
  122. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/base.py +0 -0
  123. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/coverage.py +0 -0
  124. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/delivery_report.py +0 -0
  125. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/fohm.py +0 -0
  126. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/genotype.py +0 -0
  127. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/gens.py +0 -0
  128. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/gisaid.py +0 -0
  129. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/mutacc.py +0 -0
  130. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/nipt/__init__.py +0 -0
  131. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/nipt/base.py +0 -0
  132. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/nipt/ftp.py +0 -0
  133. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/nipt/statina.py +0 -0
  134. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/observations/__init__.py +0 -0
  135. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/observations/observations.py +0 -0
  136. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/observations/utils.py +0 -0
  137. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/scout.py +0 -0
  138. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/utils.py +0 -0
  139. {cg-83.18.0 → cg-83.18.1}/cg/cli/upload/validate.py +0 -0
  140. {cg-83.18.0 → cg-83.18.1}/cg/cli/utils.py +0 -0
  141. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/__init__.py +0 -0
  142. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/balsamic/__init__.py +0 -0
  143. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/balsamic/base.py +0 -0
  144. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/balsamic/options.py +0 -0
  145. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/balsamic/pon.py +0 -0
  146. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/balsamic/umi.py +0 -0
  147. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/base.py +0 -0
  148. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/commands.py +0 -0
  149. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/fluffy/__init__.py +0 -0
  150. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/fluffy/base.py +0 -0
  151. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/jasen/__init__.py +0 -0
  152. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/jasen/base.py +0 -0
  153. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/microsalt/__init__.py +0 -0
  154. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/microsalt/base.py +0 -0
  155. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip/__init__.py +0 -0
  156. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip/base.py +0 -0
  157. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip/options.py +0 -0
  158. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip_dna/__init__.py +0 -0
  159. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip_dna/base.py +0 -0
  160. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip_rna/__init__.py +0 -0
  161. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mip_rna/base.py +0 -0
  162. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mutant/__init__.py +0 -0
  163. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/mutant/base.py +0 -0
  164. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/nallo/__init__.py +0 -0
  165. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/nallo/base.py +0 -0
  166. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/nf_analysis.py +0 -0
  167. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/raredisease/__init__.py +0 -0
  168. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/raredisease/base.py +0 -0
  169. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/raw_data/__init__.py +0 -0
  170. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/raw_data/base.py +0 -0
  171. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/raw_data/raw_data_service.py +0 -0
  172. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/rnafusion/__init__.py +0 -0
  173. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/rnafusion/base.py +0 -0
  174. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/taxprofiler/__init__.py +0 -0
  175. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/taxprofiler/base.py +0 -0
  176. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/tomte/base.py +0 -0
  177. {cg-83.18.0 → cg-83.18.1}/cg/cli/workflow/utils.py +0 -0
  178. {cg-83.18.0 → cg-83.18.1}/cg/clients/__init__.py +0 -0
  179. {cg-83.18.0 → cg-83.18.1}/cg/clients/arnold/api.py +0 -0
  180. {cg-83.18.0 → cg-83.18.1}/cg/clients/arnold/dto/create_case_request.py +0 -0
  181. {cg-83.18.0 → cg-83.18.1}/cg/clients/arnold/exceptions.py +0 -0
  182. {cg-83.18.0 → cg-83.18.1}/cg/clients/chanjo2/__init__.py +0 -0
  183. {cg-83.18.0 → cg-83.18.1}/cg/clients/chanjo2/client.py +0 -0
  184. {cg-83.18.0 → cg-83.18.1}/cg/clients/chanjo2/models.py +0 -0
  185. {cg-83.18.0 → cg-83.18.1}/cg/clients/chanjo2/utils.py +0 -0
  186. {cg-83.18.0 → cg-83.18.1}/cg/clients/freshdesk/__init__.py +0 -0
  187. {cg-83.18.0 → cg-83.18.1}/cg/clients/freshdesk/constants.py +0 -0
  188. {cg-83.18.0 → cg-83.18.1}/cg/clients/freshdesk/exceptions.py +0 -0
  189. {cg-83.18.0 → cg-83.18.1}/cg/clients/freshdesk/freshdesk_client.py +0 -0
  190. {cg-83.18.0 → cg-83.18.1}/cg/clients/freshdesk/models.py +0 -0
  191. {cg-83.18.0 → cg-83.18.1}/cg/clients/freshdesk/utils.py +0 -0
  192. {cg-83.18.0 → cg-83.18.1}/cg/clients/janus/__init__.py +0 -0
  193. {cg-83.18.0 → cg-83.18.1}/cg/clients/janus/api.py +0 -0
  194. {cg-83.18.0 → cg-83.18.1}/cg/clients/janus/dto/__init__.py +0 -0
  195. {cg-83.18.0 → cg-83.18.1}/cg/clients/janus/dto/create_qc_metrics_request.py +0 -0
  196. {cg-83.18.0 → cg-83.18.1}/cg/clients/janus/exceptions.py +0 -0
  197. {cg-83.18.0 → cg-83.18.1}/cg/constants/__init__.py +0 -0
  198. {cg-83.18.0 → cg-83.18.1}/cg/constants/archiving.py +0 -0
  199. {cg-83.18.0 → cg-83.18.1}/cg/constants/backup.py +0 -0
  200. {cg-83.18.0 → cg-83.18.1}/cg/constants/cli_options.py +0 -0
  201. {cg-83.18.0 → cg-83.18.1}/cg/constants/compression.py +0 -0
  202. {cg-83.18.0 → cg-83.18.1}/cg/constants/constants.py +0 -0
  203. {cg-83.18.0 → cg-83.18.1}/cg/constants/delivery.py +0 -0
  204. {cg-83.18.0 → cg-83.18.1}/cg/constants/demultiplexing.py +0 -0
  205. {cg-83.18.0 → cg-83.18.1}/cg/constants/devices.py +0 -0
  206. {cg-83.18.0 → cg-83.18.1}/cg/constants/encryption.py +0 -0
  207. {cg-83.18.0 → cg-83.18.1}/cg/constants/extraction.py +0 -0
  208. {cg-83.18.0 → cg-83.18.1}/cg/constants/file_transfer_service.py +0 -0
  209. {cg-83.18.0 → cg-83.18.1}/cg/constants/gene_panel.py +0 -0
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  776. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/pacbio_long_read/constants.py +0 -0
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  786. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/rml/models/order.py +0 -0
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  789. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/rna_fusion/constants.py +0 -0
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  793. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/rna_fusion/validation_rules.py +0 -0
  794. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/taxprofiler/constants.py +0 -0
  795. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/taxprofiler/models/order.py +0 -0
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  797. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/taxprofiler/validation_rules.py +0 -0
  798. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/tomte/constants.py +0 -0
  799. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/tomte/models/case.py +0 -0
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  802. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/order_types/tomte/validation_rules.py +0 -0
  803. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/response_mapper.py +0 -0
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  805. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case/__init__.py +0 -0
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  807. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case/utils.py +0 -0
  808. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/__init__.py +0 -0
  809. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/pedigree/__init__.py +0 -0
  810. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/pedigree/models.py +0 -0
  811. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/pedigree/utils.py +0 -0
  812. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/pedigree/validate_pedigree.py +0 -0
  813. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/rules.py +0 -0
  814. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/case_sample/utils.py +0 -0
  815. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/order/__init__.py +0 -0
  816. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/order/rules.py +0 -0
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  818. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/rules/sample/rules.py +0 -0
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  822. {cg-83.18.0 → cg-83.18.1}/cg/services/orders/validation/utils.py +0 -0
  823. {cg-83.18.0 → cg-83.18.1}/cg/services/pdc_service/__init__.py +0 -0
  824. {cg-83.18.0 → cg-83.18.1}/cg/services/pdc_service/pdc_service.py +0 -0
  825. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/__init__.py +0 -0
  826. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/abstract_classes.py +0 -0
  827. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/abstract_models.py +0 -0
  828. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/constants.py +0 -0
  829. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/error_handler.py +0 -0
  830. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/exc.py +0 -0
  831. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/__init__.py +0 -0
  832. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py +0 -0
  833. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/data_transfer_service/__init__.py +0 -0
  834. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py +0 -0
  835. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/data_transfer_service/dto.py +0 -0
  836. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/data_transfer_service/utils.py +0 -0
  837. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/housekeeper_service/models.py +0 -0
  838. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/housekeeper_service/pacbio_houskeeper_service.py +0 -0
  839. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/metrics_parser/__init__.py +0 -0
  840. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/metrics_parser/metrics_parser.py +0 -0
  841. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/metrics_parser/models.py +0 -0
  842. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/metrics_parser/utils.py +0 -0
  843. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/post_processing_service.py +0 -0
  844. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/run_data_generator/pacbio_run_data_generator.py +0 -0
  845. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/run_data_generator/run_data.py +0 -0
  846. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/run_file_manager/models.py +0 -0
  847. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/run_file_manager/run_file_manager.py +0 -0
  848. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/run_validator/pacbio_run_validator.py +0 -0
  849. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/pacbio/sequencing_runs_service.py +0 -0
  850. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/run_names/__init__.py +0 -0
  851. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/run_names/pacbio.py +0 -0
  852. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/run_names/service.py +0 -0
  853. {cg-83.18.0 → cg-83.18.1}/cg/services/run_devices/validators.py +0 -0
  854. {cg-83.18.0 → cg-83.18.1}/cg/services/sample_run_metrics_service/__init__.py +0 -0
  855. {cg-83.18.0 → cg-83.18.1}/cg/services/sample_run_metrics_service/dtos.py +0 -0
  856. {cg-83.18.0 → cg-83.18.1}/cg/services/sample_run_metrics_service/sample_run_metrics_service.py +0 -0
  857. {cg-83.18.0 → cg-83.18.1}/cg/services/sample_run_metrics_service/utils.py +0 -0
  858. {cg-83.18.0 → cg-83.18.1}/cg/services/sequencing_qc_service/__init__.py +0 -0
  859. {cg-83.18.0 → cg-83.18.1}/cg/services/sequencing_qc_service/quality_checks/checks.py +0 -0
  860. {cg-83.18.0 → cg-83.18.1}/cg/services/sequencing_qc_service/quality_checks/utils.py +0 -0
  861. {cg-83.18.0 → cg-83.18.1}/cg/services/sequencing_qc_service/sequencing_qc_service.py +0 -0
  862. {cg-83.18.0 → cg-83.18.1}/cg/services/sequencing_qc_service/utils.py +0 -0
  863. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_service/__init__.py +0 -0
  864. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_service/slurm_cli_service.py +0 -0
  865. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_service/slurm_service.py +0 -0
  866. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_upload_service/__init__.py +0 -0
  867. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_upload_service/slurm_upload_config.py +0 -0
  868. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_upload_service/slurm_upload_service.py +0 -0
  869. {cg-83.18.0 → cg-83.18.1}/cg/services/slurm_upload_service/utils.py +0 -0
  870. {cg-83.18.0 → cg-83.18.1}/cg/services/validate_file_transfer_service/validate_file_transfer_service.py +0 -0
  871. {cg-83.18.0 → cg-83.18.1}/cg/services/web_services/application/models.py +0 -0
  872. {cg-83.18.0 → cg-83.18.1}/cg/services/web_services/application/service.py +0 -0
  873. {cg-83.18.0 → cg-83.18.1}/cg/services/web_services/case/service.py +0 -0
  874. {cg-83.18.0 → cg-83.18.1}/cg/services/web_services/sample/dto_mappers.py +0 -0
  875. {cg-83.18.0 → cg-83.18.1}/cg/services/web_services/sample/service.py +0 -0
  876. {cg-83.18.0 → cg-83.18.1}/cg/services/web_services/sample/utils.py +0 -0
  877. {cg-83.18.0 → cg-83.18.1}/cg/store/__init__.py +0 -0
  878. {cg-83.18.0 → cg-83.18.1}/cg/store/api/data_classes.py +0 -0
  879. {cg-83.18.0 → cg-83.18.1}/cg/store/base.py +0 -0
  880. {cg-83.18.0 → cg-83.18.1}/cg/store/crud/__init__.py +0 -0
  881. {cg-83.18.0 → cg-83.18.1}/cg/store/crud/create.py +0 -0
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  883. {cg-83.18.0 → cg-83.18.1}/cg/store/crud/read.py +0 -0
  884. {cg-83.18.0 → cg-83.18.1}/cg/store/crud/update.py +0 -0
  885. {cg-83.18.0 → cg-83.18.1}/cg/store/database.py +0 -0
  886. {cg-83.18.0 → cg-83.18.1}/cg/store/exc.py +0 -0
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  891. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_application_version_filters.py +0 -0
  892. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_bed_filters.py +0 -0
  893. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_bed_version_filters.py +0 -0
  894. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_case_filters.py +0 -0
  895. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_case_sample_filters.py +0 -0
  896. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_collaboration_filters.py +0 -0
  897. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_customer_filters.py +0 -0
  898. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_illumina_flow_cell_filters.py +0 -0
  899. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_illumina_metrics_filters.py +0 -0
  900. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_illumina_sequencing_run_filters.py +0 -0
  901. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_invoice_filters.py +0 -0
  902. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_order_filters.py +0 -0
  903. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_ordertype_application_filters.py +0 -0
  904. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_organism_filters.py +0 -0
  905. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_pacbio_smrt_cell_filters.py +0 -0
  906. {cg-83.18.0 → cg-83.18.1}/cg/store/filters/status_panel_filters.py +0 -0
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  910. {cg-83.18.0 → cg-83.18.1}/cg/store/models.py +0 -0
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  912. {cg-83.18.0 → cg-83.18.1}/cg/utils/__init__.py +0 -0
  913. {cg-83.18.0 → cg-83.18.1}/cg/utils/calculations.py +0 -0
  914. {cg-83.18.0 → cg-83.18.1}/cg/utils/checksum/__init__.py +0 -0
  915. {cg-83.18.0 → cg-83.18.1}/cg/utils/checksum/checksum.py +0 -0
  916. {cg-83.18.0 → cg-83.18.1}/cg/utils/click/EnumChoice.py +0 -0
  917. {cg-83.18.0 → cg-83.18.1}/cg/utils/click/__init__.py +0 -0
  918. {cg-83.18.0 → cg-83.18.1}/cg/utils/commands.py +0 -0
  919. {cg-83.18.0 → cg-83.18.1}/cg/utils/date.py +0 -0
  920. {cg-83.18.0 → cg-83.18.1}/cg/utils/dict.py +0 -0
  921. {cg-83.18.0 → cg-83.18.1}/cg/utils/email.py +0 -0
  922. {cg-83.18.0 → cg-83.18.1}/cg/utils/enums.py +0 -0
  923. {cg-83.18.0 → cg-83.18.1}/cg/utils/files.py +0 -0
  924. {cg-83.18.0 → cg-83.18.1}/cg/utils/flask/__init__.py +0 -0
  925. {cg-83.18.0 → cg-83.18.1}/cg/utils/flask/enum.py +0 -0
  926. {cg-83.18.0 → cg-83.18.1}/cg/utils/mapping.py +0 -0
  927. {cg-83.18.0 → cg-83.18.1}/cg/utils/time.py +0 -0
  928. {cg-83.18.0 → cg-83.18.1}/cg/utils/utils.py +0 -0
{cg-83.18.0 → cg-83.18.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: cg
3
- Version: 83.18.0
3
+ Version: 83.18.1
4
4
  Summary: Clinical Genomics command center
5
5
  Requires-Python: >=3.11,<3.13
6
6
  Classifier: Programming Language :: Python
cg-83.18.1/cg/__init__.py ADDED
@@ -0,0 +1,2 @@
1
+ __title__ = "cg"
2
+ __version__ = "83.18.1"
{cg-83.18.0 → cg-83.18.1}/cg/constants/nf_analysis.py RENAMED
@@ -24,6 +24,7 @@ RAREDISEASE_METRIC_CONDITIONS_WES: dict[str, dict[str, Any]] = {
24
24
  "GC_DROPOUT": {"norm": "lt", "threshold": 10},
25
25
  RAREDISEASE_PREDICTED_SEX_METRIC: {"norm": "eq", "threshold": None},
26
26
  "gender": {"norm": "eq", "threshold": None},
27
+ "FREEMIX": {"norm": "lt", "threshold": 0.02},
27
28
  }
28
29
 
29
30
  RAREDISEASE_METRIC_CONDITIONS_WGS: dict[str, dict[str, Any]] = {
@@ -35,6 +36,7 @@ RAREDISEASE_METRIC_CONDITIONS_WGS: dict[str, dict[str, Any]] = {
35
36
  "GC_DROPOUT": {"norm": "lt", "threshold": 5},
36
37
  RAREDISEASE_PREDICTED_SEX_METRIC: {"norm": "eq", "threshold": None},
37
38
  "gender": {"norm": "eq", "threshold": None},
39
+ "FREEMIX": {"norm": "lt", "threshold": 0.02},
38
40
  }
39
41
 
40
42
  RAREDISEASE_PARENT_PEDDY_METRIC_CONDITION: dict[str, dict[str, Any]] = {
{cg-83.18.0 → cg-83.18.1}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
4
4
 
5
5
  [project]
6
6
  name = "cg"
7
- version = "83.18.0"
7
+ version = "83.18.1"
8
8
  description = "Clinical Genomics command center"
9
9
  readme = {file = "README.md", content-type = "text/markdown"}
10
10
  homepage = "https://github.com/Clinical-Genomics/cg"
cg-83.18.0/cg/__init__.py DELETED
@@ -1,2 +0,0 @@
1
- __title__ = "cg"
2
- __version__ = "83.18.0"
{cg-83.18.0 → cg-83.18.1}/README.md RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/__init__.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/coverage/api.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/__init__.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/crunchy.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/files.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/models.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/crunchy/sbatch.py RENAMED
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{cg-83.18.0 → cg-83.18.1}/cg/apps/demultiplex/sbatch.py RENAMED
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