optional liftover_root and its handling

README.md

@@ -20,6 +20,9 @@ region_file: # str (path to a conflict file)
 alternative_haplotype_vcf: # str (path to a vcf file with known SVs, e.g.
 from the HGSVC)
 
+# path to liftover directory (explained below)
+liftover_root: # default to 'resources/references/liftover'
+
 # Settings for the pairwise alignment
 pw_alignment:
   match: # positive integer
@@ -52,6 +55,7 @@ references/
                 t2t_v1.0_to_t2t_v1.1.chain
                 liftover_config.json
 ```
+
 where `liftover_config.json` looks like:
 ```json
 {

workflow/Snakefile

@@ -3,12 +3,16 @@ from pathlib import Path
 import sys
 sys.path.append("./workflow/scripts")
 
-regionfile = config['region_file']
+regionfile = config["region_file"]
 ref_dict = config["ref_dict"]
 references = list(ref_dict.keys())
 ref_files = list(ref_dict.values())
 main_reference = config["main_ref_name"]
-liftover_config = Path(config["liftover_root"]) / "liftover_config.json"
+try:
+    liftover_root = config["liftover_root"]
+except:
+    liftover_root = "resources/references/liftover/"
+liftover_config = Path(liftover_root) / "liftover_config.json"
 
 
 from conflict_positions import Region
@@ -127,7 +131,7 @@ rule create_igv_batch:
         "results/{sample}/{region}/igv_batch_{ref}.txt"
     params:
         region = lambda wc: f"{Region(wc.get('region')):}",
-        ref_file = lambda wc: ref_dict[wc.get('ref')],
+        ref_file = lambda wc: ref_dict[wc.get("ref")],
         path_to_resources = Path(".").absolute()
     shell:
         """