Merge pull request #180 from nf-core/empty-annotation-intersection

Make sure per-sample-tool bed files are non-empty
nf-core · Dec 16, 2024 · abdc4cb · abdc4cb
2 parents 1e16e22 + b49b8e1
commit abdc4cb
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/modules/local/annotation/templates/annotation.py b/modules/local/annotation/templates/annotation.py
@@ -47,7 +47,6 @@ def format_yaml_like(data: dict, indent: int = 0) -> str:
 except pd.errors.EmptyDataError:
     raise ValueError("Intersection between circRNAs and GTF file is empty.")
 df = df.rename(columns=columns)
-df 
 
 # Extract circRNAs without match
 mask = df['feature_start'] == -1
@@ -97,7 +96,7 @@ def determine_type(row):
             return "circRNA"
     if "intron" in row["feature_type"]:
         return "ciRNA"
-    
+
     return "unknown-circRNA"
 
 def get_representation(row, column):

diff --git a/subworkflows/local/bsj_detection.nf b/subworkflows/local/bsj_detection.nf
@@ -109,6 +109,9 @@ workflow BSJ_DETECTION {
         ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool.mix(MAPSPLICE.out.bed)
     }
 
+    ch_bsj_bed_per_sample_tool = ch_bsj_bed_per_sample_tool
+        .filter{ meta, bed -> !bed.isEmpty() }
+
     //
     // QUANTIFY BSJs PER TOOL
     //