cg 80.1.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

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Files changed (91) hide show
  1. cg/__init__.py +1 -1
  2. cg/apps/housekeeper/hk.py +1 -1
  3. cg/apps/tb/api.py +1 -1
  4. cg/cli/upload/mutacc.py +16 -3
  5. cg/cli/upload/scout.py +2 -2
  6. cg/cli/upload/utils.py +10 -1
  7. cg/cli/workflow/balsamic/base.py +29 -4
  8. cg/cli/workflow/microsalt/base.py +3 -1
  9. cg/cli/workflow/nallo/base.py +18 -38
  10. cg/cli/workflow/nf_analysis.py +2 -203
  11. cg/cli/workflow/raredisease/base.py +33 -51
  12. cg/cli/workflow/rnafusion/base.py +28 -3
  13. cg/cli/workflow/taxprofiler/base.py +21 -13
  14. cg/cli/workflow/tomte/base.py +17 -19
  15. cg/constants/constants.py +3 -3
  16. cg/constants/devices.py +6 -1
  17. cg/constants/gene_panel.py +3 -1
  18. cg/constants/lims.py +4 -0
  19. cg/constants/orderforms.py +1 -1
  20. cg/constants/pacbio.py +1 -0
  21. cg/constants/scout.py +6 -4
  22. cg/exc.py +12 -4
  23. cg/meta/compress/compress.py +7 -2
  24. cg/meta/delivery_report/nallo.py +1 -1
  25. cg/meta/delivery_report/templates/macros/ticket_system.html +1 -1
  26. cg/meta/observations/balsamic_observations_api.py +1 -1
  27. cg/meta/observations/mip_dna_observations_api.py +1 -1
  28. cg/meta/observations/nallo_observations_api.py +1 -1
  29. cg/meta/observations/observations_api.py +1 -1
  30. cg/meta/observations/raredisease_observations_api.py +1 -1
  31. cg/meta/tar/tar.py +5 -2
  32. cg/meta/upload/coverage.py +5 -5
  33. cg/meta/upload/raredisease/raredisease.py +3 -0
  34. cg/meta/upload/scout/nallo_config_builder.py +14 -0
  35. cg/meta/workflow/nallo.py +22 -95
  36. cg/meta/workflow/nf_analysis.py +11 -262
  37. cg/meta/workflow/raredisease.py +3 -112
  38. cg/meta/workflow/rnafusion.py +2 -34
  39. cg/meta/workflow/taxprofiler.py +2 -38
  40. cg/meta/workflow/tomte.py +2 -42
  41. cg/models/deliverables/metric_deliverables.py +1 -1
  42. cg/models/nallo/nallo.py +14 -64
  43. cg/models/nf_analysis.py +1 -41
  44. cg/models/raredisease/raredisease.py +0 -62
  45. cg/models/rnafusion/rnafusion.py +0 -26
  46. cg/models/scout/scout_load_config.py +1 -0
  47. cg/models/taxprofiler/taxprofiler.py +0 -42
  48. cg/models/tomte/tomte.py +0 -69
  49. cg/resources/nallo_bundle_filenames.yaml +282 -22
  50. cg/resources/raredisease_bundle_filenames.yaml +11 -1
  51. cg/resources/taxprofiler_bundle_filenames.yaml +20 -0
  52. cg/server/admin.py +51 -24
  53. cg/server/app.py +15 -4
  54. cg/server/endpoints/sequencing_run/dtos.py +21 -3
  55. cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py +29 -10
  56. cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py +20 -0
  57. cg/services/analysis_starter/configurator/configurator.py +1 -1
  58. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/models.py +40 -1
  59. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/nallo.py +3 -1
  60. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/tomte_params_file_creator.py +3 -1
  61. cg/services/analysis_starter/factories/configurator_factory.py +4 -4
  62. cg/services/analysis_starter/tracker/implementations/balsamic.py +4 -1
  63. cg/services/analysis_starter/tracker/implementations/microsalt.py +4 -4
  64. cg/services/analysis_starter/tracker/implementations/mip_dna.py +4 -1
  65. cg/services/analysis_starter/tracker/implementations/nextflow_tracker.py +6 -4
  66. cg/services/analysis_starter/tracker/tracker.py +10 -6
  67. cg/services/illumina/backup/backup_service.py +29 -7
  68. cg/services/orders/validation/constants.py +3 -0
  69. cg/services/orders/validation/index_sequences.py +558 -0
  70. cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py +39 -18
  71. cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py +8 -2
  72. cg/services/run_devices/pacbio/data_transfer_service/dto.py +9 -3
  73. cg/services/run_devices/pacbio/data_transfer_service/utils.py +14 -7
  74. cg/services/run_devices/pacbio/metrics_parser/models.py +1 -0
  75. cg/services/run_devices/pacbio/sequencing_runs_service.py +35 -7
  76. cg/services/sequencing_qc_service/quality_checks/checks.py +18 -16
  77. cg/services/sequencing_qc_service/quality_checks/utils.py +82 -18
  78. cg/services/sequencing_qc_service/sequencing_qc_service.py +12 -10
  79. cg/store/crud/create.py +73 -42
  80. cg/store/crud/read.py +50 -2
  81. cg/store/crud/update.py +14 -3
  82. cg/store/models.py +88 -31
  83. cg/store/store.py +8 -1
  84. {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/METADATA +1 -1
  85. {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/RECORD +91 -90
  86. /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{nallo.py → nallo_sample_sheet_creator.py} +0 -0
  87. /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{raredisease.py → raredisease_sample_sheet_creator.py} +0 -0
  88. /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{rnafusion.py → rnafusion_sample_sheet_creator.py} +0 -0
  89. /cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{taxprofiler.py → taxprofiler_sample_sheet_creator.py} +0 -0
  90. {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/WHEEL +0 -0
  91. {cg-80.1.0.dist-info → cg-83.14.0.dist-info}/entry_points.txt +0 -0
cg/resources/nallo_bundle_filenames.yaml CHANGED
@@ -28,34 +28,284 @@
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  path: PATHTOCASE/assembly/sample/SAMPLEID/SAMPLEID_aligned_assembly.bam.bai
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  step: assembly
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  tag: assembly_aligned_index
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr1.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr2.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr3.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr4.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr5.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr6.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr7.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr8.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr9.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr10.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr11.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr12.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr13.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr14.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr15.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr16.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr17.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr18.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr19.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr20.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr21.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chr22.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chrX.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chrY.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_coverage_chrM.png
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+ step: chromograph_cov
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+ tag: tcov
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr1.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr2.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr3.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr4.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr5.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr6.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr7.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr8.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr9.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr10.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr11.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr12.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr13.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr14.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr15.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr16.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr17.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr18.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr19.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr20.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr21.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chr22.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chrX.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chrY.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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+ - format: png
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+ id: SAMPLEID
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+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chrM.png
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+ step: chromograph_rhoviz
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+ tag: autozyg
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  - format: bed
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  id: SAMPLEID
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- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz
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+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz
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  step: methylation_pileup
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  tag: hap1
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  - format: bed
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  id: SAMPLEID
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- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz.tbi
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+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz.tbi
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  step: methylation_pileup
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  tag: hap1_index
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  - format: bed
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  id: SAMPLEID
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- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz
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+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz
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  step: methylation_pileup
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  tag: hap2
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  - format: bed
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  id: SAMPLEID
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- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz.tbi
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+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz.tbi
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  step: methylation_pileup
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  tag: hap2_index
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  - format: bed
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  id: SAMPLEID
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- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz
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+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz
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  step: methylation_pileup
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  tag: ungrouped
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  - format: bed
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  id: SAMPLEID
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- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz.tbi
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+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz.tbi
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  step: methylation_pileup
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  tag: ungrouped_index
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  - format: meta
@@ -160,77 +410,87 @@
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  tag: vcf_str_index
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  - format: meta
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  id: CASEID
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- path: /home/proj/production/workflows/nallo/references/v0.3.1/grch38_trgt_pathogenic_repeats.bed
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+ path: /home/proj/production/workflows/nallo/references/v0.4.0/grch38_trgt_pathogenic_repeats.bed
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  step: trgt
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  tag: variant_catalog
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  - format: vcf
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  id: CASEID
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- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked.vcf.gz
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+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_research.vcf.gz
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  step: snv_annotated
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  tag: vcf_snv_research
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  - format: vcf
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  id: CASEID
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- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked.vcf.gz.tbi
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+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_research.vcf.gz.tbi
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  step: snv_annotated
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  tag: vcf_snv_research_index
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  - format: vcf
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  id: CASEID
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- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz
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+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_clinical.vcf.gz
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  step: snv_annotated_filtered
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  tag: vcf_snv_clinical
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431
  - format: vcf
182
432
  id: CASEID
183
- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz.tbi
433
+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_clinical.vcf.gz.tbi
184
434
  step: snv_annotated_filtered
185
435
  tag: vcf_snv_clinical_index
186
436
  - format: vcf
187
437
  id: CASEID
188
- path: PATHTOCASE/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked.vcf.gz
438
+ path: PATHTOCASE/svs/family/CASEID/CASEID_svs_annotated_ranked_research.vcf.gz
189
439
  step: sv_annotated_ranked
190
440
  tag: vcf_sv_research
191
441
  - format: vcf
192
442
  id: CASEID
193
- path: PATHTOCASE/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked.vcf.gz.tbi
443
+ path: PATHTOCASE/svs/family/CASEID/CASEID_svs_annotated_ranked_research.vcf.gz.tbi
194
444
  step: sv_annotated_ranked
195
445
  tag: vcf_sv_research_index
196
446
  - format: vcf
197
447
  id: CASEID
198
- path: PATHTOCASE/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz
448
+ path: PATHTOCASE/svs/family/CASEID/CASEID_svs_annotated_ranked_clinical.vcf.gz
199
449
  step: sv_annotated_ranked_filtered
200
450
  tag: vcf_sv_clinical
201
451
  - format: vcf
202
452
  id: CASEID
203
- path: PATHTOCASE/svs/family/CASEID/CASEID_svs_cnvs_merged_annotated_ranked_filtered.vcf.gz.tbi
453
+ path: PATHTOCASE/svs/family/CASEID/CASEID_svs_annotated_ranked_clinical.vcf.gz.tbi
204
454
  step: sv_annotated_ranked_filtered
205
455
  tag: vcf_sv_clinical_index
206
456
  - format: vcf
207
457
  id: CASEID
208
- path: PATHTOCASE/svs/family/CASEID/CASEID_hificnv_cnvs_merged.vcf.gz
458
+ path: PATHTOCASE/svs/family/CASEID/CASEID_hificnv_svs.vcf.gz
209
459
  step: svs_per_caller
210
460
  tag: vcf_hificnv
211
461
  - format: vcf
212
462
  id: CASEID
213
- path: PATHTOCASE/svs/family/CASEID/CASEID_hificnv_cnvs_merged.vcf.gz.tbi
463
+ path: PATHTOCASE/svs/family/CASEID/CASEID_hificnv_svs.vcf.gz.tbi
214
464
  step: svs_per_caller
215
465
  tag: vcf_hificnv_index
216
466
  - format: vcf
217
467
  id: CASEID
218
- path: PATHTOCASE/svs/family/CASEID/CASEID_severus_svs_merged.vcf.gz
468
+ path: PATHTOCASE/svs/family/CASEID/CASEID_sawfish_svs.vcf.gz
469
+ step: svs_per_caller
470
+ tag: vcf_sawfish
471
+ - format: vcf
472
+ id: CASEID
473
+ path: PATHTOCASE/svs/family/CASEID/CASEID_sawfish_svs.vcf.gz.tbi
474
+ step: svs_per_caller
475
+ tag: vcf_sawfish_index
476
+ - format: vcf
477
+ id: CASEID
478
+ path: PATHTOCASE/svs/family/CASEID/CASEID_severus_svs.vcf.gz
219
479
  step: svs_per_caller
220
480
  tag: vcf_severus
221
481
  - format: vcf
222
482
  id: CASEID
223
- path: PATHTOCASE/svs/family/CASEID/CASEID_severus_svs_merged.vcf.gz.tbi
483
+ path: PATHTOCASE/svs/family/CASEID/CASEID_severus_svs.vcf.gz.tbi
224
484
  step: svs_per_caller
225
485
  tag: vcf_severus_index
226
486
  - format: vcf
227
487
  id: CASEID
228
- path: PATHTOCASE/svs/family/CASEID/CASEID_sniffles_svs_merged.vcf.gz
488
+ path: PATHTOCASE/svs/family/CASEID/CASEID_sniffles_svs.vcf.gz
229
489
  step: svs_per_caller
230
490
  tag: vcf_sniffles
231
491
  - format: vcf
232
492
  id: CASEID
233
- path: PATHTOCASE/svs/family/CASEID/CASEID_sniffles_svs_merged.vcf.gz.tbi
493
+ path: PATHTOCASE/svs/family/CASEID/CASEID_sniffles_svs.vcf.gz.tbi
234
494
  step: svs_per_caller
235
495
  tag: vcf_sniffles_index
236
496
  - format: meta
@@ -290,7 +550,7 @@
290
550
  tag: manifest
291
551
  - format: yml
292
552
  id: CASEID
293
- path: PATHTOCASE/pipeline_info/nallo_pipeline_software_mqc_versions.yml
553
+ path: PATHTOCASE/pipeline_info/nallo_software_mqc_versions.yml
294
554
  step: software-versions
295
555
  tag: software-versions
296
556
  - format: yaml
cg/resources/raredisease_bundle_filenames.yaml CHANGED
@@ -28,6 +28,11 @@
28
28
  path: PATHTOCASE/qc_bam/SAMPLEID.d4
29
29
  step: qc_bam
30
30
  tag: d4tools_d4
31
+ - format: meta
32
+ id: SAMPLEID
33
+ path: PATHTOCASE/qc_bam/SAMPLEID_sambamba_depth.bed
34
+ step: qc_bam
35
+ tag: sambamba_depth
31
36
  - format: png
32
37
  id: SAMPLEID
33
38
  path: PATHTOCASE/qc_bam/SAMPLEID_chromographcov/SAMPLEID_tidditcov_1.png
@@ -160,7 +165,7 @@
160
165
  tag: json
161
166
  - format: meta
162
167
  id: CASEID
163
- path: /home/proj/production/workflows/raredisease/references/references_2.0.1_mtp_1/grch37_expansionhunter_variant_catalog_-5.0.0-.json
168
+ path: /home/proj/production/workflows/raredisease/references/v1.0/grch37_expansionhunter_variant_catalog_-5.0.0-.json
164
169
  step: expansionhunter
165
170
  tag: variant_catalog
166
171
  - format: vcf
@@ -253,6 +258,11 @@
253
258
  path: PATHTOCASE/call_snv/genome/CASEID_snv.vcf.gz.tbi
254
259
  step: call_snv
255
260
  tag: call_snv_index
261
+ - format: meta
262
+ id: SAMPLEID
263
+ path: PATHTOCASE/call_snv/genome/SAMPLEID_deepvar.visual_report.html
264
+ step: deepvariant
265
+ tag: report
256
266
  - format: vcf
257
267
  id: CASEID
258
268
  path: PATHTOCASE/call_snv/mitochondria/CASEID_mitochondria.vcf.gz
cg/resources/taxprofiler_bundle_filenames.yaml CHANGED
@@ -8,6 +8,11 @@
8
8
  path: PATHTOCASE/kraken2/k2_pluspf/SAMPLENAME_pe_k2_pluspf.kraken2.kraken2.report.txt
9
9
  step: kraken2
10
10
  tag: kraken2_report
11
+ - format: txt
12
+ id: SAMPLEID
13
+ path: PATHTOCASE/kraken2/k2_pluspf/SAMPLENAME_pe_k2_pluspf.kraken2.kraken2.classifiedreads.txt
14
+ step: kraken2
15
+ tag: kraken2_classified_reads
11
16
  - format: html
12
17
  id: CASEID
13
18
  path: PATHTOCASE/krona/kraken2_k2_pluspf.html
@@ -38,6 +43,11 @@
38
43
  path: PATHTOCASE/centrifuge/p_compressed+h+v/SAMPLENAME_pe_p_compressed+h+v.centrifuge.txt
39
44
  step: centrifuge
40
45
  tag: centrifuge_report
46
+ - format: txt
47
+ id: SAMPLEID
48
+ path: PATHTOCASE/centrifuge/p_compressed+h+v/SAMPLENAME_pe_p_compressed+h+v.centrifuge.results.txt
49
+ step: centrifuge
50
+ tag: centrifuge_results
41
51
  - format: html
42
52
  id: CASEID
43
53
  path: PATHTOCASE/multiqc/multiqc_report.html
@@ -83,3 +93,13 @@
83
93
  path: PATHTOCASE/manifest.json
84
94
  step: manifest
85
95
  tag: manifest
96
+ - format: tsv
97
+ id: CASEID
98
+ path: PATHTOCASE/taxpasta/kraken2_k2_pluspf.tsv
99
+ step: taxpasta
100
+ tag: kraken2
101
+ - format: tsv
102
+ id: CASEID
103
+ path: PATHTOCASE/taxpasta/centrifuge_p_compressed+h+v.tsv
104
+ step: taxpasta
105
+ tag: centrifuge
cg/server/admin.py CHANGED
@@ -12,11 +12,11 @@ from wtforms.form import Form
12
12
 
13
13
  from cg.constants.constants import NG_UL_SUFFIX, CaseActions, DataDelivery, Workflow
14
14
  from cg.models.orders.constants import OrderType
15
+ from cg.server.app_config import app_config
15
16
  from cg.server.ext import applications_service, db, sample_service
16
17
  from cg.server.utils import MultiCheckboxField
17
18
  from cg.store.models import Application
18
19
  from cg.utils.flask.enum import SelectEnumField
19
- from cg.server.app_config import app_config
20
20
 
21
21
 
22
22
  class BaseView(ModelView):
@@ -112,12 +112,6 @@ def view_pacbio_sample_sequencing_metrics_link(unused1, unused2, model, unused3)
112
112
  )
113
113
 
114
114
 
115
- def is_external_application(unused1, unused2, model, unused3):
116
- """column formatter to open this view"""
117
- del unused1, unused2, unused3
118
- return model.application_version.application.is_external if model.application_version else ""
119
-
120
-
121
115
  def view_order_types(unused1, unused2, model, unused3):
122
116
  del unused1, unused2, unused3
123
117
  order_type_list = "<br>".join(model.order_types)
@@ -246,6 +240,8 @@ class ApplicationView(BaseView):
246
240
  "is_accredited",
247
241
  "target_reads",
248
242
  "percent_reads_guaranteed",
243
+ "target_hifi_yield",
244
+ "percent_hifi_yield_guaranteed",
249
245
  "comment",
250
246
  "prep_category",
251
247
  "sequencing_depth",
@@ -306,10 +302,11 @@ class ApplicationView(BaseView):
306
302
  def on_model_change(self, form: Form, model: Application, is_created: bool):
307
303
  """Override to persist entries to the OrderTypeApplication table."""
308
304
  super(ApplicationView, self).on_model_change(form=form, model=model, is_created=is_created)
309
- order_types: list[OrderType] = form["suitable_order_types"].data
310
- applications_service.update_application_order_types(
311
- application=model, order_types=order_types
312
- )
305
+ if "suitable_order_types" in form.data:
306
+ order_types: list[OrderType] = form["suitable_order_types"].data
307
+ applications_service.update_application_order_types(
308
+ application=model, order_types=order_types
309
+ )
313
310
 
314
311
  def edit_form(self, obj=None):
315
312
  """Override to prefill the order types according to the current Application entry."""
@@ -734,10 +731,36 @@ class PoolView(BaseView):
734
731
  class SampleView(BaseView):
735
732
  """Admin view for Model.Sample"""
736
733
 
737
- column_exclude_list = [
738
- "age_at_sampling",
739
- "_phenotype_groups",
740
- "_phenotype_terms",
734
+ column_list = [
735
+ "application_version",
736
+ "customer",
737
+ "organism",
738
+ "invoice",
739
+ "is_cancelled",
740
+ "capture_kit",
741
+ "comment",
742
+ "control",
743
+ "created_at",
744
+ "delivered_at",
745
+ "downsampled_to",
746
+ "from_sample",
747
+ "internal_id",
748
+ "is_tumour",
749
+ "loqusdb_id",
750
+ "name",
751
+ "no_invoice",
752
+ "order",
753
+ "ordered_at",
754
+ "original_ticket",
755
+ "prepared_at",
756
+ "priority",
757
+ "reads",
758
+ "hifi_yield",
759
+ "last_sequenced_at",
760
+ "received_at",
761
+ "reference_genome",
762
+ "sex",
763
+ "subject_id",
741
764
  ]
742
765
  column_default_sort = ("created_at", True)
743
766
  column_editable_list = [
@@ -757,7 +780,6 @@ class SampleView(BaseView):
757
780
  column_formatters = {
758
781
  "application_version": view_application_link_via_application_version,
759
782
  "customer": view_customer_link,
760
- "is_external": is_external_application,
761
783
  "internal_id": view_case_sample_link,
762
784
  "invoice": InvoiceView.view_invoice_link,
763
785
  "original_ticket": view_ticket_link,
@@ -878,12 +900,12 @@ class IlluminaSampleSequencingMetricsView(BaseView):
878
900
  column_searchable_list = ["sample.internal_id", "instrument_run.device.internal_id"]
879
901
 
880
902
 
881
- class PacbioSmrtCellView(BaseView):
903
+ class PacbioSmrtCellMetricsView(BaseView):
882
904
  """Admin view for Model.PacbioSMRTCell"""
883
905
 
884
906
  column_list = (
885
907
  "internal_id",
886
- "run_name",
908
+ "sequencing_run.run_name",
887
909
  "movie_name",
888
910
  "well",
889
911
  "plate",
@@ -907,8 +929,9 @@ class PacbioSmrtCellView(BaseView):
907
929
  "internal_id": view_pacbio_sample_sequencing_metrics_link,
908
930
  "model": view_smrt_cell_model,
909
931
  }
932
+ column_labels = {"sequencing_run.run_name": "Run Name"}
910
933
  column_default_sort = ("completed_at", True)
911
- column_searchable_list = ["device.internal_id", "run_name", "movie_name"]
934
+ column_searchable_list = ["device.internal_id", "movie_name", "sequencing_run.run_name"]
912
935
  column_sortable_list = [
913
936
  ("internal_id", "device.internal_id"),
914
937
  "started_at",
@@ -924,7 +947,7 @@ class PacbioSmrtCellView(BaseView):
924
947
  "<a href='%s'>%s</a>"
925
948
  % (
926
949
  url_for(
927
- "pacbiosequencingrun.index_view",
950
+ "pacbiosmrtcellmetrics.index_view",
928
951
  search=model.instrument_run.device.internal_id,
929
952
  ),
930
953
  model.instrument_run.device.internal_id,
@@ -936,19 +959,22 @@ class PacbioSmrtCellView(BaseView):
936
959
 
937
960
 
938
961
  class PacbioSampleRunMetricsView(BaseView):
939
- column_filters = ["instrument_run.run_name", "instrument_run.plate"]
962
+ column_filters = [
963
+ "instrument_run.plate",
964
+ "instrument_run.sequencing_run.run_name",
965
+ ]
940
966
  column_formatters = {
941
- "smrt_cell": PacbioSmrtCellView.view_smrt_cell_link,
967
+ "smrt_cell": PacbioSmrtCellMetricsView.view_smrt_cell_link,
942
968
  "sample": SampleView.view_sample_link,
943
969
  }
944
970
  column_labels = {
945
- "instrument_run.run_name": "Run name",
946
971
  "instrument_run.plate": "Plate",
972
+ "instrument_run.sequencing_run.run_name": "Run Name",
947
973
  }
948
974
  column_list = [
949
975
  "smrt_cell",
950
976
  "sample",
951
- "instrument_run.run_name",
977
+ "instrument_run.sequencing_run.run_name",
952
978
  "instrument_run.plate",
953
979
  "hifi_reads",
954
980
  "hifi_yield",
@@ -958,4 +984,5 @@ class PacbioSampleRunMetricsView(BaseView):
958
984
  column_searchable_list = [
959
985
  "sample.internal_id",
960
986
  "instrument_run.device.internal_id",
987
+ "instrument_run.sequencing_run.run_name",
961
988
  ]
cg/server/app.py CHANGED
@@ -19,7 +19,12 @@ from cg.server.endpoints.sequencing_metrics.illumina_sequencing_metrics import F
19
19
  from cg.server.endpoints.sequencing_metrics.pacbio_sequencing_metrics import (
20
20
  PACBIO_SAMPLE_SEQUENCING_METRICS_BLUEPRINT,
21
21
  )
22
- from cg.server.endpoints.sequencing_run.pacbio_sequencing_run import PACBIO_SEQUENCING_RUN_BLUEPRINT
22
+ from cg.server.endpoints.sequencing_run.pacbio_sequencing_run import (
23
+ PACBIO_SEQUENCING_RUNS_BLUEPRINT,
24
+ )
25
+ from cg.server.endpoints.sequencing_run.pacbio_smrt_cell_metrics import (
26
+ PACBIO_SMRT_CELL_METRICS_BLUEPRINT,
27
+ )
23
28
  from cg.server.endpoints.users import USERS_BLUEPRINT
24
29
  from cg.store.database import get_scoped_session_registry
25
30
  from cg.store.models import (
@@ -39,7 +44,7 @@ from cg.store.models import (
39
44
  Order,
40
45
  Organism,
41
46
  PacbioSampleSequencingMetrics,
42
- PacbioSequencingRun,
47
+ PacbioSMRTCellMetrics,
43
48
  Panel,
44
49
  Pool,
45
50
  Sample,
@@ -107,7 +112,8 @@ def _register_blueprints(app: Flask):
107
112
  app.register_blueprint(ANALYSES_BLUEPRINT)
108
113
  app.register_blueprint(USERS_BLUEPRINT)
109
114
  app.register_blueprint(PACBIO_SAMPLE_SEQUENCING_METRICS_BLUEPRINT)
110
- app.register_blueprint(PACBIO_SEQUENCING_RUN_BLUEPRINT)
115
+ app.register_blueprint(PACBIO_SEQUENCING_RUNS_BLUEPRINT)
116
+ app.register_blueprint(PACBIO_SMRT_CELL_METRICS_BLUEPRINT)
111
117
  app.register_blueprint(INDEX_SEQUENCES_BLUEPRINT)
112
118
  _register_admin_views()
113
119
 
@@ -119,6 +125,7 @@ def _register_blueprints(app: Flask):
119
125
  ext.csrf.exempt(FLOW_CELLS_BLUEPRINT)
120
126
  ext.csrf.exempt(ANALYSES_BLUEPRINT)
121
127
  ext.csrf.exempt(USERS_BLUEPRINT)
128
+ ext.csrf.exempt(PACBIO_SEQUENCING_RUNS_BLUEPRINT)
122
129
 
123
130
  @app.route("/")
124
131
  def index():
@@ -158,7 +165,11 @@ def _register_admin_views():
158
165
  ext.admin.add_view(
159
166
  admin.IlluminaSampleSequencingMetricsView(IlluminaSampleSequencingMetrics, ext.db.session)
160
167
  )
161
- ext.admin.add_view(admin.PacbioSmrtCellView(PacbioSequencingRun, ext.db.session))
168
+ ext.admin.add_view(
169
+ admin.PacbioSmrtCellMetricsView(
170
+ PacbioSMRTCellMetrics, ext.db.session, "Pacbio SMRT Cell Metrics"
171
+ )
172
+ )
162
173
  ext.admin.add_view(
163
174
  admin.PacbioSampleRunMetricsView(PacbioSampleSequencingMetrics, ext.db.session)
164
175
  )