Fix for simulation

snakecnv/detection.snk

@@ -91,8 +91,9 @@ tools = config['tools']
 # list of chromosomes
 chromosomes = config["chromosomes"]
 chr_batches = {}
+ref_chr = "reference_raw.fasta" if not os.path.exists(REFERENCE) and os.path.exists("reference_raw.fasta") else REFERENCE
 for chromosome in chromosomes:
-    chr_batches[chromosome] = get_chr_batches(REFERENCE, chromosome)
+    chr_batches[chromosome] = get_chr_batches(ref_chr, chromosome)
 
 # list of variants to be detected
 varianttypes = ['DEL', 'INV', 'DUP', 'mCNV']