update snakemake

mortazavilab · Sep 4, 2024 · cabff57 · cabff57
1 parent 0213923
commit cabff57
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Showing 5 changed files with 149 additions and 26 deletions.
diff --git a/Topyfic/utilsMakeModel.py b/Topyfic/utilsMakeModel.py
@@ -145,7 +145,7 @@ def subset_data(data, keep, loc='var'):
 
 def calculate_leiden_clustering(trains,
                                 data,
-                                n_top_genes=50,
+                                n_top_genes=None,
                                 resolution=1,
                                 max_iter_harmony=10,
                                 min_cell_participation=None,

diff --git a/workflow/snakemake/config/config.yaml b/workflow/snakemake/config/config.yaml
@@ -28,7 +28,7 @@ train:
                   90, 91, 92, 93, 94, 95, 96, 97, 98, 99]
 
 top_model:
-  n_top_genes: 50
+  n_top_genes: None
   resolution: 1
   max_iter_harmony: 10
   min_cell_participation: None

diff --git a/workflow/snakemake/resources/analysing.ipynb b/workflow/snakemake/resources/analysing.ipynb
diff --git a/workflow/snakemake/workflow/rules/topModel.smk b/workflow/snakemake/workflow/rules/topModel.smk
@@ -25,7 +25,7 @@ rule run_top_model:
 
         make_topmodel.make_top_model(trains=[train],
             adata_paths=config['count_adata'][params.name],
-            n_top_genes=int(config['top_model']['n_top_genes']),
+            n_top_genes=None if config['top_model']['n_top_genes'] == "None" else int(config['top_model']['n_top_genes']),
             resolution=float(config['top_model']['resolution']),
             max_iter_harmony=int(config['top_model']['max_iter_harmony']),
             min_cell_participation=None if config['top_model']['min_cell_participation'] == "None" else float(

diff --git a/workflow/snakemake/workflow/rules/train.smk b/workflow/snakemake/workflow/rules/train.smk
@@ -33,6 +33,6 @@ rule run_train_model:
         make_train.make_train_model(name=params.name,
             adata_path=config['count_adata'][params.name],
             k=int(params.n_topic),
-            n_runs=config['train']['n_runs'],
+            n_runs=int(config['train']['n_runs']),
             random_state=config['train']['random_states'],
             train_output=f"{config['workdir']}/{params.name}/{params.n_topic}/train/")