patch for getting chromsomes in get_batches

snakecnv/mergebatches.snk

@@ -55,7 +55,9 @@ def get_batches(wdir):
                         # Search for chromosomes:
                         my_chrs = []
                         for ffile in glob(os.path.join(filter_dir, variant, "svtyper_*_%s_genotypes_filtered.vcf.gz" % variant)):
-                            chrm = ffile.split("_")[1]
+                            # chrm = ffile.split("_")[1] doesn't work when the directory path contains an "_"
+                            basefilename = os.path.basename(ffile)
+                            chrm = basefilename.split("_")[1]
                             my_chrs.append(chrm)
 
                         if len(my_chrs) == 0:
@@ -188,4 +190,4 @@ rule summary:
         1
     shell:
         "cp {params.ipynb} {output.ipynb}; "
-        "jupyter nbconvert --to html --template {params.tpl} --execute {output.ipynb}"
\ No newline at end of file
+        "jupyter nbconvert --to html --template {params.tpl} --execute {output.ipynb}"