chore: Snakemake setup all

BoevaLab · Jun 26, 2024 · 312e425 · 312e425
1 parent 17aa02a
commit 312e425
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Showing 58 changed files with 3,225 additions and 4,597 deletions.
diff --git a/paper/config.json → config/config.json b/paper/config.json → config/config.json
@@ -1,5 +1,8 @@
 {
     "random_state": 42,
+    "datasets_last": [
+        "BLCA"
+    ],
     "datasets": [
         "BLCA",
         "BRCA",
@@ -12,8 +15,9 @@
         "OV",
         "STAD"
     ],
-    "datasets_last": ["LUSC"],
-    "datasets_lel": ["BLCA"],
+    "datasets_lel": [
+        "BLCA"
+    ],
     "n_outer_splits": 5,
     "n_outer_repetitions": 25,
     "pc_n_components": 16,
@@ -25,7 +29,15 @@
     "seed": 42,
     "shuffle_cv": true,
     "timing_reps": 5,
-    "l1_ratio_tuned": [0.1, 0.5, 0.7, 0.9, 0.95, 0.99, 1],
+    "l1_ratio_tuned": [
+        0.1,
+        0.5,
+        0.7,
+        0.9,
+        0.95,
+        0.99,
+        1
+    ],
     "pc_n_components_tuned": [
         8,
         16,
@@ -66,7 +78,9 @@
         0.4,
         0.6
     ],
-    "tune_batch_size": [1024],
+    "tune_batch_size": [
+        1024
+    ],
     "random_search_n_iter": 50,
     "error_score": 100
 }
diff --git a/config/config.yaml b/config/config.yaml
@@ -0,0 +1,8 @@
+snakemake_min_version: "7.30.1"
+mambaforge_version: "23.3.1-0"
+config_path: "config/config.json"
+datasets:
+  ["BLCA", "BRCA", "HNSC", "KIRC", "LGG", "LIHC", "LUAD", "LUSC", "OV", "STAD"]
+random_seed: 42
+n_outer_repetitions: 25
+n_outer_splits: 5
diff --git a/paper/.Rprofile b/paper/.Rprofile
diff --git a/paper/README.md b/paper/README.md
diff --git a/paper/paper.Rproj b/paper/paper.Rproj