diff --git a/snakecnv/tools/pindel.snk b/snakecnv/tools/pindel.snk
index bbdf1e4549794114d163b8a11b6fe171fb4877ec..fdfdab365ca348edb0c2358235e55c276459c3f1 100644
--- a/snakecnv/tools/pindel.snk
+++ b/snakecnv/tools/pindel.snk
@@ -67,7 +67,7 @@ rule mergepindelbatches:
     threads:
         1
     shell:
-        "mergepindelbatches.py {output.D} {input.D} 1>{log.stdout} 2>{log.stderr}; "
-        "mergepindelbatches.py {output.INV} {input.INV} 1>>{log.stdout} 2>>{log.stderr}; "
-        "mergepindelbatches.py {output.TD} {input.TD} 1>>{log.stdout} 2>>{log.stderr}; "
+        "mergepindelbatches.py {output.D} {input.D} 1>{log.stdout} 2>{log.stderr};\n"
+        "mergepindelbatches.py {output.INV} {input.INV} 1>>{log.stdout} 2>>{log.stderr};\n"
+        "mergepindelbatches.py {output.TD} {input.TD} 1>>{log.stdout} 2>>{log.stderr};\n"
         "rm -rf {wildcards.batch}/pindel/{wildcards.chrom}"
\ No newline at end of file