Fix doublet removal problem that occurs when only one method is active

nf-core · Jun 15, 2024 · c192cbf · c192cbf
1 parent 6b6c524
commit c192cbf
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Showing 2 changed files with 19 additions and 17 deletions.
diff --git a/modules/local/doublet_detection/doublet_removal/main.nf b/modules/local/doublet_detection/doublet_removal/main.nf
@@ -13,7 +13,7 @@ process DOUBLET_REMOVAL {
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
-    path("*_mqc.json")             , emit: multiqc_files
+    path("*_mqc.json")             , emit: multiqc_files, optional: true
     path "versions.yml"            , emit: versions
 
     when:

diff --git a/modules/local/doublet_detection/doublet_removal/templates/doublet_removal.py b/modules/local/doublet_detection/doublet_removal/templates/doublet_removal.py
@@ -44,6 +44,24 @@ def load(path: str) -> pd.DataFrame:
 adata = adata[mask, :]
 adata.write_h5ad(f"{prefix}.h5ad")
 
+# Versions
+
+versions = {
+    "${task.process}": {
+        "python": platform.python_version(),
+        "anndata": ad.__version__,
+        "pandas": pd.__version__,
+        "matplotlib": matplotlib.__version__,
+        "upsetplot": upsetplot.__version__,
+    }
+}
+
+with open("versions.yml", "w") as f:
+    f.write(format_yaml_like(versions))
+
+if not len(predictions.columns) > 1:
+    exit(0)
+
 # Plot
 
 contents = {column: predictions[column][predictions[column]].index.tolist()
@@ -77,19 +95,3 @@ def load(path: str) -> pd.DataFrame:
     }
 
     json.dump(custom_json, f_json)
-
-
-# Versions
-
-versions = {
-    "${task.process}": {
-        "python": platform.python_version(),
-        "anndata": ad.__version__,
-        "pandas": pd.__version__,
-        "matplotlib": matplotlib.__version__,
-        "upsetplot": upsetplot.__version__,
-    }
-}
-
-with open("versions.yml", "w") as f:
-    f.write(format_yaml_like(versions))