reorganize directories for pipeline running from pretrained models

PMBio · May 16, 2024 · 3238e39 · 3238e39
1 parent 6067e5f
commit 3238e39
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Showing 42 changed files with 2 additions and 2 deletions.
diff --git a/pipelines/association_testing_pretrained.snakefile b/pipelines/association_testing_pretrained.snakefile
@@ -16,7 +16,7 @@ n_repeats = config['n_repeats']
 debug = '--debug ' if debug_flag else ''
 do_scoretest = '--do-scoretest ' if config.get('do_scoretest', False) else ''
 tensor_compression_level = config['training'].get('tensor_compression_level', 1)
-model_path = Path(config.get("pretrained_model_path", "pretrained_models/models"))
+model_path = Path(config.get("pretrained_model_path", "pretrained_models"))
 
 wildcard_constraints:
     repeat="\d+",

diff --git a/pipelines/association_testing_pretrained_regenie.snakefile b/pipelines/association_testing_pretrained_regenie.snakefile
@@ -12,7 +12,7 @@ n_bags = config['training']['n_bags'] if not debug_flag else 3
 n_repeats = config['n_repeats']
 debug = '--debug ' if debug_flag else ''
 do_scoretest = '--do-scoretest ' if config.get('do_scoretest', False) else ''
-model_path = Path(config.get("pretrained_model_path", "pretrained_models/models"))
+model_path = Path(config.get("pretrained_model_path", "pretrained_models"))
 
 wildcard_constraints:
     repeat="\d+",

diff --git a/...ed_models/models/repeat_0/best/bag_0.ckpt → pretrained_models/repeat_0/best/bag_0.ckpt b/...ed_models/models/repeat_0/best/bag_0.ckpt → pretrained_models/repeat_0/best/bag_0.ckpt
diff --git a/...ed_models/models/repeat_1/best/bag_0.ckpt → pretrained_models/repeat_1/best/bag_0.ckpt b/...ed_models/models/repeat_1/best/bag_0.ckpt → pretrained_models/repeat_1/best/bag_0.ckpt
diff --git a/...s/models/repeat_1/best/bag_0.ckpt.reverse → ...d_models/repeat_1/best/bag_0.ckpt.reverse b/...s/models/repeat_1/best/bag_0.ckpt.reverse → ...d_models/repeat_1/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_10/best/bag_0.ckpt → pretrained_models/repeat_10/best/bag_0.ckpt b/...d_models/models/repeat_10/best/bag_0.ckpt → pretrained_models/repeat_10/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_11/best/bag_0.ckpt → pretrained_models/repeat_11/best/bag_0.ckpt b/...d_models/models/repeat_11/best/bag_0.ckpt → pretrained_models/repeat_11/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_12/best/bag_0.ckpt → pretrained_models/repeat_12/best/bag_0.ckpt b/...d_models/models/repeat_12/best/bag_0.ckpt → pretrained_models/repeat_12/best/bag_0.ckpt
diff --git a/.../models/repeat_12/best/bag_0.ckpt.reverse → ..._models/repeat_12/best/bag_0.ckpt.reverse b/.../models/repeat_12/best/bag_0.ckpt.reverse → ..._models/repeat_12/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_13/best/bag_0.ckpt → pretrained_models/repeat_13/best/bag_0.ckpt b/...d_models/models/repeat_13/best/bag_0.ckpt → pretrained_models/repeat_13/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_14/best/bag_0.ckpt → pretrained_models/repeat_14/best/bag_0.ckpt b/...d_models/models/repeat_14/best/bag_0.ckpt → pretrained_models/repeat_14/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_15/best/bag_0.ckpt → pretrained_models/repeat_15/best/bag_0.ckpt b/...d_models/models/repeat_15/best/bag_0.ckpt → pretrained_models/repeat_15/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_16/best/bag_0.ckpt → pretrained_models/repeat_16/best/bag_0.ckpt b/...d_models/models/repeat_16/best/bag_0.ckpt → pretrained_models/repeat_16/best/bag_0.ckpt
diff --git a/.../models/repeat_16/best/bag_0.ckpt.reverse → ..._models/repeat_16/best/bag_0.ckpt.reverse b/.../models/repeat_16/best/bag_0.ckpt.reverse → ..._models/repeat_16/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_17/best/bag_0.ckpt → pretrained_models/repeat_17/best/bag_0.ckpt b/...d_models/models/repeat_17/best/bag_0.ckpt → pretrained_models/repeat_17/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_18/best/bag_0.ckpt → pretrained_models/repeat_18/best/bag_0.ckpt b/...d_models/models/repeat_18/best/bag_0.ckpt → pretrained_models/repeat_18/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_19/best/bag_0.ckpt → pretrained_models/repeat_19/best/bag_0.ckpt b/...d_models/models/repeat_19/best/bag_0.ckpt → pretrained_models/repeat_19/best/bag_0.ckpt
diff --git a/...ed_models/models/repeat_2/best/bag_0.ckpt → pretrained_models/repeat_2/best/bag_0.ckpt b/...ed_models/models/repeat_2/best/bag_0.ckpt → pretrained_models/repeat_2/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_20/best/bag_0.ckpt → pretrained_models/repeat_20/best/bag_0.ckpt b/...d_models/models/repeat_20/best/bag_0.ckpt → pretrained_models/repeat_20/best/bag_0.ckpt
diff --git a/.../models/repeat_20/best/bag_0.ckpt.reverse → ..._models/repeat_20/best/bag_0.ckpt.reverse b/.../models/repeat_20/best/bag_0.ckpt.reverse → ..._models/repeat_20/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_21/best/bag_0.ckpt → pretrained_models/repeat_21/best/bag_0.ckpt b/...d_models/models/repeat_21/best/bag_0.ckpt → pretrained_models/repeat_21/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_22/best/bag_0.ckpt → pretrained_models/repeat_22/best/bag_0.ckpt b/...d_models/models/repeat_22/best/bag_0.ckpt → pretrained_models/repeat_22/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_23/best/bag_0.ckpt → pretrained_models/repeat_23/best/bag_0.ckpt b/...d_models/models/repeat_23/best/bag_0.ckpt → pretrained_models/repeat_23/best/bag_0.ckpt
diff --git a/.../models/repeat_23/best/bag_0.ckpt.reverse → ..._models/repeat_23/best/bag_0.ckpt.reverse b/.../models/repeat_23/best/bag_0.ckpt.reverse → ..._models/repeat_23/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_24/best/bag_0.ckpt → pretrained_models/repeat_24/best/bag_0.ckpt b/...d_models/models/repeat_24/best/bag_0.ckpt → pretrained_models/repeat_24/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_25/best/bag_0.ckpt → pretrained_models/repeat_25/best/bag_0.ckpt b/...d_models/models/repeat_25/best/bag_0.ckpt → pretrained_models/repeat_25/best/bag_0.ckpt
diff --git a/.../models/repeat_25/best/bag_0.ckpt.reverse → ..._models/repeat_25/best/bag_0.ckpt.reverse b/.../models/repeat_25/best/bag_0.ckpt.reverse → ..._models/repeat_25/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_26/best/bag_0.ckpt → pretrained_models/repeat_26/best/bag_0.ckpt b/...d_models/models/repeat_26/best/bag_0.ckpt → pretrained_models/repeat_26/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_27/best/bag_0.ckpt → pretrained_models/repeat_27/best/bag_0.ckpt b/...d_models/models/repeat_27/best/bag_0.ckpt → pretrained_models/repeat_27/best/bag_0.ckpt
diff --git a/.../models/repeat_27/best/bag_0.ckpt.reverse → ..._models/repeat_27/best/bag_0.ckpt.reverse b/.../models/repeat_27/best/bag_0.ckpt.reverse → ..._models/repeat_27/best/bag_0.ckpt.reverse
diff --git a/...d_models/models/repeat_28/best/bag_0.ckpt → pretrained_models/repeat_28/best/bag_0.ckpt b/...d_models/models/repeat_28/best/bag_0.ckpt → pretrained_models/repeat_28/best/bag_0.ckpt
diff --git a/...d_models/models/repeat_29/best/bag_0.ckpt → pretrained_models/repeat_29/best/bag_0.ckpt b/...d_models/models/repeat_29/best/bag_0.ckpt → pretrained_models/repeat_29/best/bag_0.ckpt
diff --git a/...ed_models/models/repeat_3/best/bag_0.ckpt → pretrained_models/repeat_3/best/bag_0.ckpt b/...ed_models/models/repeat_3/best/bag_0.ckpt → pretrained_models/repeat_3/best/bag_0.ckpt
diff --git a/...ed_models/models/repeat_4/best/bag_0.ckpt → pretrained_models/repeat_4/best/bag_0.ckpt b/...ed_models/models/repeat_4/best/bag_0.ckpt → pretrained_models/repeat_4/best/bag_0.ckpt
diff --git a/...ed_models/models/repeat_5/best/bag_0.ckpt → pretrained_models/repeat_5/best/bag_0.ckpt b/...ed_models/models/repeat_5/best/bag_0.ckpt → pretrained_models/repeat_5/best/bag_0.ckpt
diff --git a/...s/models/repeat_5/best/bag_0.ckpt.reverse → ...d_models/repeat_5/best/bag_0.ckpt.reverse b/...s/models/repeat_5/best/bag_0.ckpt.reverse → ...d_models/repeat_5/best/bag_0.ckpt.reverse
diff --git a/...ed_models/models/repeat_6/best/bag_0.ckpt → pretrained_models/repeat_6/best/bag_0.ckpt b/...ed_models/models/repeat_6/best/bag_0.ckpt → pretrained_models/repeat_6/best/bag_0.ckpt
diff --git a/...s/models/repeat_6/best/bag_0.ckpt.reverse → ...d_models/repeat_6/best/bag_0.ckpt.reverse b/...s/models/repeat_6/best/bag_0.ckpt.reverse → ...d_models/repeat_6/best/bag_0.ckpt.reverse
diff --git a/...ed_models/models/repeat_7/best/bag_0.ckpt → pretrained_models/repeat_7/best/bag_0.ckpt b/...ed_models/models/repeat_7/best/bag_0.ckpt → pretrained_models/repeat_7/best/bag_0.ckpt
diff --git a/...s/models/repeat_7/best/bag_0.ckpt.reverse → ...d_models/repeat_7/best/bag_0.ckpt.reverse b/...s/models/repeat_7/best/bag_0.ckpt.reverse → ...d_models/repeat_7/best/bag_0.ckpt.reverse
diff --git a/...ed_models/models/repeat_8/best/bag_0.ckpt → pretrained_models/repeat_8/best/bag_0.ckpt b/...ed_models/models/repeat_8/best/bag_0.ckpt → pretrained_models/repeat_8/best/bag_0.ckpt
diff --git a/...ed_models/models/repeat_9/best/bag_0.ckpt → pretrained_models/repeat_9/best/bag_0.ckpt b/...ed_models/models/repeat_9/best/bag_0.ckpt → pretrained_models/repeat_9/best/bag_0.ckpt