cg 76.0.0__py3-none-any.whl → 83.14.0__py3-none-any.whl

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 (152) hide show
  1. cg/__init__.py +1 -1
  2. cg/apps/housekeeper/hk.py +18 -1
  3. cg/apps/tb/api.py +42 -5
  4. cg/cli/transfer.py +13 -2
  5. cg/cli/upload/mutacc.py +16 -3
  6. cg/cli/upload/scout.py +2 -2
  7. cg/cli/upload/utils.py +10 -1
  8. cg/cli/workflow/balsamic/base.py +86 -172
  9. cg/cli/workflow/balsamic/options.py +3 -48
  10. cg/cli/workflow/balsamic/umi.py +210 -15
  11. cg/cli/workflow/microsalt/base.py +4 -2
  12. cg/cli/workflow/mip_dna/base.py +1 -1
  13. cg/cli/workflow/nallo/base.py +73 -23
  14. cg/cli/workflow/nf_analysis.py +5 -207
  15. cg/cli/workflow/raredisease/base.py +41 -54
  16. cg/cli/workflow/rnafusion/base.py +38 -8
  17. cg/cli/workflow/taxprofiler/base.py +31 -18
  18. cg/cli/workflow/tomte/base.py +83 -10
  19. cg/constants/constants.py +25 -30
  20. cg/constants/devices.py +6 -1
  21. cg/constants/gene_panel.py +3 -1
  22. cg/constants/housekeeper_tags.py +28 -28
  23. cg/constants/lims.py +4 -0
  24. cg/constants/nf_analysis.py +0 -1
  25. cg/constants/observations.py +21 -5
  26. cg/constants/orderforms.py +3 -3
  27. cg/constants/pacbio.py +1 -0
  28. cg/constants/priority.py +1 -1
  29. cg/constants/report.py +1 -0
  30. cg/constants/scout.py +12 -9
  31. cg/constants/sequencing.py +2 -2
  32. cg/constants/tb.py +5 -5
  33. cg/exc.py +27 -5
  34. cg/meta/compress/compress.py +7 -2
  35. cg/meta/delivery_report/balsamic.py +3 -1
  36. cg/meta/delivery_report/delivery_report_api.py +4 -3
  37. cg/meta/delivery_report/nallo.py +11 -11
  38. cg/meta/delivery_report/raredisease.py +7 -3
  39. cg/meta/delivery_report/templates/macros/data_analysis/qc_metrics/balsamic_qc_metrics.html +1 -0
  40. cg/meta/delivery_report/templates/macros/ticket_system.html +1 -1
  41. cg/meta/observations/balsamic_observations_api.py +110 -14
  42. cg/meta/observations/mip_dna_observations_api.py +1 -1
  43. cg/meta/observations/nallo_observations_api.py +1 -1
  44. cg/meta/observations/observations_api.py +23 -32
  45. cg/meta/observations/raredisease_observations_api.py +1 -1
  46. cg/meta/tar/tar.py +5 -2
  47. cg/meta/transfer/lims.py +32 -3
  48. cg/meta/upload/balsamic/balsamic.py +1 -8
  49. cg/meta/upload/coverage.py +5 -5
  50. cg/meta/upload/raredisease/raredisease.py +3 -0
  51. cg/meta/upload/scout/hk_tags.py +1 -0
  52. cg/meta/upload/scout/nallo_config_builder.py +31 -7
  53. cg/meta/workflow/balsamic.py +70 -36
  54. cg/meta/workflow/fastq.py +8 -0
  55. cg/meta/workflow/microsalt/quality_controller/models.py +0 -2
  56. cg/meta/workflow/microsalt/quality_controller/quality_controller.py +8 -16
  57. cg/meta/workflow/microsalt/quality_controller/result_logger.py +3 -6
  58. cg/meta/workflow/microsalt/quality_controller/utils.py +2 -45
  59. cg/meta/workflow/nallo.py +21 -99
  60. cg/meta/workflow/nf_analysis.py +12 -263
  61. cg/meta/workflow/raredisease.py +3 -112
  62. cg/meta/workflow/rnafusion.py +2 -34
  63. cg/meta/workflow/taxprofiler.py +2 -38
  64. cg/meta/workflow/tomte.py +2 -42
  65. cg/models/balsamic/config.py +0 -24
  66. cg/models/balsamic/metrics.py +5 -3
  67. cg/models/cg_config.py +39 -16
  68. cg/models/deliverables/metric_deliverables.py +1 -1
  69. cg/models/delivery_report/metadata.py +2 -1
  70. cg/models/nallo/nallo.py +14 -64
  71. cg/models/nf_analysis.py +1 -41
  72. cg/models/raredisease/raredisease.py +1 -63
  73. cg/models/rnafusion/rnafusion.py +0 -26
  74. cg/models/scout/scout_load_config.py +5 -2
  75. cg/models/taxprofiler/taxprofiler.py +0 -42
  76. cg/models/tomte/tomte.py +0 -69
  77. cg/resources/nallo_bundle_filenames.yaml +292 -22
  78. cg/resources/raredisease_bundle_filenames.yaml +11 -1
  79. cg/resources/taxprofiler_bundle_filenames.yaml +20 -0
  80. cg/server/admin.py +106 -25
  81. cg/server/app.py +15 -4
  82. cg/server/endpoints/sequencing_run/dtos.py +21 -3
  83. cg/server/endpoints/sequencing_run/pacbio_sequencing_run.py +29 -10
  84. cg/server/endpoints/sequencing_run/pacbio_smrt_cell_metrics.py +20 -0
  85. cg/services/analysis_starter/{service.py → analysis_starter.py} +11 -9
  86. cg/services/analysis_starter/configurator/abstract_model.py +8 -0
  87. cg/services/analysis_starter/configurator/configurator.py +1 -1
  88. cg/services/analysis_starter/configurator/extensions/nallo.py +27 -0
  89. cg/services/analysis_starter/configurator/extensions/{abstract.py → pipeline_extension.py} +1 -1
  90. cg/services/analysis_starter/configurator/extensions/raredisease.py +3 -1
  91. cg/services/analysis_starter/configurator/extensions/tomte_extension.py +28 -0
  92. cg/services/analysis_starter/configurator/file_creators/balsamic_config.py +240 -0
  93. cg/services/analysis_starter/configurator/file_creators/gene_panel.py +10 -5
  94. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/abstract.py +2 -1
  95. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/models.py +40 -1
  96. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/nallo.py +37 -0
  97. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/raredisease.py +8 -5
  98. cg/services/analysis_starter/configurator/file_creators/nextflow/params_file/tomte_params_file_creator.py +64 -0
  99. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/creator.py +1 -1
  100. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/nallo_sample_sheet_creator.py +65 -0
  101. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/protocol.py +12 -0
  102. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{raredisease.py → raredisease_sample_sheet_creator.py} +2 -2
  103. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{rnafusion.py → rnafusion_sample_sheet_creator.py} +2 -2
  104. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/{taxprofiler.py → taxprofiler_sample_sheet_creator.py} +2 -2
  105. cg/services/analysis_starter/configurator/file_creators/nextflow/sample_sheet/tomte_sample_sheet_creator.py +36 -0
  106. cg/services/analysis_starter/configurator/implementations/balsamic.py +68 -0
  107. cg/services/analysis_starter/configurator/implementations/nextflow.py +22 -5
  108. cg/services/analysis_starter/configurator/models/balsamic.py +152 -0
  109. cg/services/analysis_starter/configurator/models/mip_dna.py +6 -8
  110. cg/services/analysis_starter/configurator/models/nextflow.py +9 -0
  111. cg/services/analysis_starter/constants.py +2 -0
  112. cg/services/analysis_starter/factories/configurator_factory.py +131 -51
  113. cg/services/analysis_starter/factories/starter_factory.py +36 -7
  114. cg/services/analysis_starter/input_fetcher/implementations/bam_fetcher.py +57 -0
  115. cg/services/analysis_starter/input_fetcher/implementations/fastq_fetcher.py +3 -3
  116. cg/services/analysis_starter/submitters/seqera_platform/{client.py → seqera_platform_client.py} +19 -3
  117. cg/services/analysis_starter/submitters/seqera_platform/seqera_platform_submitter.py +73 -0
  118. cg/services/analysis_starter/submitters/submitter.py +1 -1
  119. cg/services/analysis_starter/submitters/subprocess/submitter.py +2 -1
  120. cg/services/analysis_starter/tracker/implementations/balsamic.py +22 -0
  121. cg/services/analysis_starter/tracker/implementations/microsalt.py +4 -4
  122. cg/services/analysis_starter/tracker/implementations/mip_dna.py +4 -1
  123. cg/services/analysis_starter/tracker/implementations/{nextflow.py → nextflow_tracker.py} +6 -4
  124. cg/services/analysis_starter/tracker/tracker.py +19 -15
  125. cg/services/deliver_files/factory.py +1 -1
  126. cg/services/delivery_message/messages/__init__.py +24 -14
  127. cg/services/delivery_message/messages/{microsalt_mwr_message.py → microsalt_message.py} +1 -1
  128. cg/services/delivery_message/utils.py +4 -40
  129. cg/services/illumina/backup/backup_service.py +29 -7
  130. cg/services/orders/validation/constants.py +3 -0
  131. cg/services/orders/validation/index_sequences.py +558 -0
  132. cg/services/orders/validation/order_types/microsalt/models/sample.py +2 -3
  133. cg/services/run_devices/pacbio/data_storage_service/pacbio_store_service.py +39 -18
  134. cg/services/run_devices/pacbio/data_transfer_service/data_transfer_service.py +8 -2
  135. cg/services/run_devices/pacbio/data_transfer_service/dto.py +9 -3
  136. cg/services/run_devices/pacbio/data_transfer_service/utils.py +14 -7
  137. cg/services/run_devices/pacbio/metrics_parser/models.py +1 -0
  138. cg/services/run_devices/pacbio/sequencing_runs_service.py +35 -7
  139. cg/services/sequencing_qc_service/quality_checks/checks.py +18 -16
  140. cg/services/sequencing_qc_service/quality_checks/utils.py +82 -18
  141. cg/services/sequencing_qc_service/sequencing_qc_service.py +12 -10
  142. cg/store/crud/create.py +73 -42
  143. cg/store/crud/read.py +73 -7
  144. cg/store/crud/update.py +14 -3
  145. cg/store/models.py +98 -35
  146. cg/store/store.py +8 -1
  147. {cg-76.0.0.dist-info → cg-83.14.0.dist-info}/METADATA +1 -1
  148. {cg-76.0.0.dist-info → cg-83.14.0.dist-info}/RECORD +150 -138
  149. cg/services/analysis_starter/submitters/seqera_platform/submitter.py +0 -39
  150. cg/services/delivery_message/messages/microsalt_mwx_message.py +0 -18
  151. {cg-76.0.0.dist-info → cg-83.14.0.dist-info}/WHEEL +0 -0
  152. {cg-76.0.0.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
269
+ step: chromograph_rhoviz
270
+ tag: autozyg
271
+ - format: png
272
+ id: SAMPLEID
273
+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chrY.png
274
+ step: chromograph_rhoviz
275
+ tag: autozyg
276
+ - format: png
277
+ id: SAMPLEID
278
+ path: PATHTOCASE/images/chromograph/sample/SAMPLEID/SAMPLEID_chromograph_autozyg_chrM.png
279
+ step: chromograph_rhoviz
280
+ tag: autozyg
31
281
  - format: bed
32
282
  id: SAMPLEID
33
- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz
283
+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz
34
284
  step: methylation_pileup
35
285
  tag: hap1
36
286
  - format: bed
37
287
  id: SAMPLEID
38
- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz.tbi
288
+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz.tbi
39
289
  step: methylation_pileup
40
290
  tag: hap1_index
41
291
  - format: bed
42
292
  id: SAMPLEID
43
- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz
293
+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz
44
294
  step: methylation_pileup
45
295
  tag: hap2
46
296
  - format: bed
47
297
  id: SAMPLEID
48
- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz.tbi
298
+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz.tbi
49
299
  step: methylation_pileup
50
300
  tag: hap2_index
51
301
  - format: bed
52
302
  id: SAMPLEID
53
- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz
303
+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz
54
304
  step: methylation_pileup
55
305
  tag: ungrouped
56
306
  - format: bed
57
307
  id: SAMPLEID
58
- path: PATHTOCASE/methylation/modkit/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz.tbi
308
+ path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz.tbi
59
309
  step: methylation_pileup
60
310
  tag: ungrouped_index
61
311
  - format: meta
@@ -160,77 +410,87 @@
160
410
  tag: vcf_str_index
161
411
  - format: meta
162
412
  id: CASEID
163
- path: /home/proj/production/workflows/nallo/references/v0.3.1/grch38_trgt_pathogenic_repeats.bed
413
+ path: /home/proj/production/workflows/nallo/references/v0.4.0/grch38_trgt_pathogenic_repeats.bed
164
414
  step: trgt
165
415
  tag: variant_catalog
166
416
  - format: vcf
167
417
  id: CASEID
168
- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked.vcf.gz
418
+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_research.vcf.gz
169
419
  step: snv_annotated
170
420
  tag: vcf_snv_research
171
421
  - format: vcf
172
422
  id: CASEID
173
- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked.vcf.gz.tbi
423
+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_research.vcf.gz.tbi
174
424
  step: snv_annotated
175
425
  tag: vcf_snv_research_index
176
426
  - format: vcf
177
427
  id: CASEID
178
- path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_filtered.vcf.gz
428
+ path: PATHTOCASE/snvs/family/CASEID/CASEID_snvs_annotated_ranked_clinical.vcf.gz
179
429
  step: snv_annotated_filtered
180
430
  tag: vcf_snv_clinical
181
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
@@ -248,6 +508,16 @@
248
508
  path: PATHTOCASE/visualization_tracks/SAMPLEID/SAMPLEID_hificnv.maf.bw
249
509
  step: maf_depth_track
250
510
  tag: bigwig
511
+ - format: meta
512
+ id: SAMPLEID
513
+ path: PATHTOCASE/qc/phasing_stats/SAMPLEID/SAMPLEID_stats.blocks.gtf.gz
514
+ step: phase_blocks
515
+ tag: gtf
516
+ - format: meta
517
+ id: SAMPLEID
518
+ path: PATHTOCASE/qc/phasing_stats/SAMPLEID/SAMPLEID_stats.blocks.gtf.gz.tbi
519
+ step: phase_blocks
520
+ tag: gtf_index
251
521
  - format: meta
252
522
  id: CASEID
253
523
  path: PATHTOCASE/multiqc/multiqc_data/multiqc_data.json
@@ -280,7 +550,7 @@
280
550
  tag: manifest
281
551
  - format: yml
282
552
  id: CASEID
283
- path: PATHTOCASE/pipeline_info/nallo_pipeline_software_mqc_versions.yml
553
+ path: PATHTOCASE/pipeline_info/nallo_software_mqc_versions.yml
284
554
  step: software-versions
285
555
  tag: software-versions
286
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