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dvc.yaml 4.8 KB

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  1. stages:
  2. select_samples:
  3. cmd: papermill -f parameters/select_samples.yaml --progress-bar --report-mode
  4. notebooks/select_samples.ipynb data/output/notebooks/select_samples.ipynb
  5. deps:
  6. - parameters/select_samples.yaml
  7. - data/input/genes/by_animal_class
  8. - data/input/species.tsv
  9. - data/input/samples.tsv
  10. - data/input/total_mtDNA_base_composition.csv
  11. - notebooks/select_samples.ipynb
  12. outs:
  13. - data/interim/selected/gestation_days
  14. - data/interim/selected/lifespan
  15. - data/interim/selected/mass_kg
  16. - data/interim/selected/metabolic_rate
  17. - data/interim/selected/mtGC
  18. - data/interim/selected/temperature
  19. - data/output/counts/species_sample_count.tsv
  20. - data/output/counts/tissue_sample_count.tsv
  21. - data/output/counts/species_tissue_sample_count.tsv
  22. - data/output/notebooks/select_samples.ipynb
  23. stage_one:
  24. cmd: papermill -f parameters/stage_one_shap_selection.yaml --progress-bar --report-mode
  25. notebooks/stage_one_shap_selection.ipynb data/output/notebooks/stage_one_shap_selection.ipynb
  26. deps:
  27. - parameters/stage_one_shap_selection.yaml
  28. - data/interim/optimization/gestation_days.sqlite
  29. - data/interim/optimization/lifespan.sqlite
  30. - data/interim/optimization/mass_kg.sqlite
  31. - data/interim/optimization/metabolic_rate.sqlite
  32. - data/interim/optimization/mtGC.sqlite
  33. - data/interim/optimization/temperature.sqlite
  34. outs:
  35. #- data/output/notebooks/stage_one_shap_selection.ipynb
  36. - data/output/plots/stage_1/
  37. - data/interim/stage_1/results_concatenated.tsv
  38. - data/interim/stage_1/partitions
  39. - data/interim/stage_2/input
  40. - data/output/stage_1/gestation_days_selected.tsv
  41. - data/output/stage_1/mass_kg_selected.tsv
  42. - data/output/stage_1/mtGC_selected.tsv
  43. - data/output/stage_1/lifespan_selected.tsv
  44. - data/output/stage_1/metabolic_rate_selected.tsv
  45. - data/output/stage_1/temperature_selected.tsv
  46. stage_two:
  47. cmd: papermill -f parameters/stage_two_shap_selection.yaml --progress-bar --report-mode
  48. notebooks/stage_two_shap_selection.ipynb data/output/notebooks/stage_two_shap_selection.ipynb
  49. deps:
  50. - data/interim/stage_1/results_concatenated.tsv
  51. - data/interim/optimization/lifespan_2.sqlite
  52. - data/interim/stage_2/input
  53. outs:
  54. - data/interim/stage_2/partitions
  55. - data/output/stage_2/lifespan_with_traits.tsv
  56. - data/output/stage_2/lifespan.tsv
  57. #- data/output/stage_2/shap_results.tsv
  58. - data/output/plots/stage_2/decision_lifespan.svg
  59. - data/output/plots/stage_2/heatmap_lifespan_unclustered.svg
  60. - data/output/plots/stage_2/summary_lifespan.svg
  61. - data/output/plots/life_history_no_genes
  62. - data/output/plots/interactions/
  63. # - data/output/notebooks/stage_two_shap_selection.ipynb
  64. stage_three:
  65. cmd: papermill -f parameters/stage_three_shap_selection.yaml --progress-bar --report-mode
  66. notebooks/stage_three_shap_selection.ipynb data/output/notebooks/stage_three_shap_selection.ipynb
  67. deps:
  68. - data/interim/optimization/lifespan_3.sqlite
  69. outs:
  70. - data/output/plots/stage_3/interactions/
  71. - data/output/plots/stage_3/life_history/
  72. - data/output/plots/stage_3/stage_3_interactions.png
  73. - data/output/plots/stage_3/stage_3_decision.svg
  74. - data/output/plots/stage_3/stage_3_summary.svg
  75. - data/output/plots/stage_3/stage_3_heatmap_unclustered.svg
  76. # - data/output/notebooks/stage_three_shap_selection.ipynb
  77. tune:
  78. cmd: python tune.py
  79. params:
  80. - parameters/tune.yaml:
  81. - trait
  82. - metrics
  83. - trials
  84. - folds
  85. - hold_outs
  86. - repeats
  87. - not_validated_species
  88. - threads
  89. - debug_local
  90. deps:
  91. - data/interim/selected/gestation_days
  92. - data/interim/selected/lifespan
  93. - data/interim/selected/mass_kg
  94. - data/interim/selected/metabolic_rate
  95. - data/interim/selected/mtGC
  96. - data/interim/selected/temperature
  97. results:
  98. cmd: papermill -f parameters/results_intersections.yaml --progress-bar --report-mode
  99. notebooks/results_intersections.ipynb data/output/notebooks/results_intersections.ipynb
  100. deps:
  101. - parameters/results_intersections.yaml
  102. - data/output/external/causality
  103. - data/output/external/linear
  104. - data/output/external/causality/causal_selection.tsv
  105. - data/output/external/causality/signature_scores_ensembl_codes.csv
  106. - notebooks/results_intersections.ipynb
  107. outs:
  108. - data/output/notebooks/results_intersections.ipynb
  109. - data/output/results/shap_with_causal_linear.tsv
  110. - data/output/stage_2/shap_results.tsv
  111. - data/output/results/shap_with_linear.tsv
  112. - data/output/results/genage_intersection.tsv
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