Easy dry run if only 1 batch

snakecnv/mergebatches.snk

@@ -2,6 +2,7 @@ import sys
 import re
 import os
 from glob import glob
+import shutil
 
 from os.path import join, isfile
 
@@ -83,6 +84,12 @@ shell.prefix("export PATH=%s/bin:\"$PATH\";" % ROOTPATH)
 
 batches, chromosomes, variant_types = get_batches(WDIR)
 
+if len(batches) == 1:
+    b_filtered = os.path.join(WDIR, "batch001", "filtered")
+    f_filtered = os.path.join(WDIR, "filtered")
+    shutil.move(b_filtered, f_filtered)
+    os.symlink(f_filtered, b_filtered)
+
 include: "tools/threads.snk"
 
 localrules: all, bamlist