Fix genomestrip rerun

snakecnv/bin/genomestrip.py

@@ -43,6 +43,10 @@ def launch(bamlist, chrom, reference, metadata, gendermap, outdir, outprefix):
     old_libpath = ":" + os.environ["LD_LIBRARY_PATH"] if "LD_LIBRARY_PATH" in os.environ else ""
     os.environ["LD_LIBRARY_PATH"] = sv_dir + "/bwa" + old_libpath
 
+    done_file = os.path.join(outprefix, "." + outprefix + ".vcf")
+    if os.path.exists(done_file):
+        os.remove(done_file)
+
     mx="-Xmx8g"
     classpath="{sv_dir}/lib/SVToolkit.jar:{sv_dir}/lib/gatk/GenomeAnalysisTK.jar:{sv_dir}/lib/gatk/Queue.jar".\
         format(sv_dir=sv_dir)