fix empty table

snakemake-workflows · Oct 26, 2023 · 5c68058 · 5c68058
1 parent 7e798b3
commit 5c68058
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/.test/config-simple/config.yaml b/.test/config-simple/config.yaml
@@ -92,7 +92,7 @@ params:
     min_alternate_fraction: 0.05 # Reduce for calling variants with lower VAFs
 
 gene_coverage:
-  min_avg_coverage: 5
+  min_avg_coverage: 0
 
 report:
   activate: true

diff --git a/workflow/scripts/coverage_table.py b/workflow/scripts/coverage_table.py
@@ -18,9 +18,12 @@
                 group_regions[(chromosome, gene)] = dict()
             group_regions[(chromosome, gene)][sample] = coverage
 
-df = pd.DataFrame.from_dict(group_regions).T
-df.index.names = ("chromosome", "gene")
-df.reset_index(inplace=True)
+if bool(group_regions):
+    df = pd.DataFrame.from_dict(group_regions).T
+    df.index.names = ("chromosome", "gene")
+    df.reset_index(inplace=True)
+else:
+    df = pd.DataFrame(columns=["chromosome", "gene"])
 
 with open(snakemake.output[0], "w") as csv_file:
     df.to_csv(csv_file, index=False, sep="\t")