Avoid hard-codig reference name

Author: ahmig

workflow/rules/vaf.smk

@@ -127,6 +127,8 @@ rule filter_tsv:
 rule tsv_to_vcf:
     threads: 1
     conda: "../envs/biopython.yaml"
+    params:
+        ref_name = config["ALIGNMENT_REFERENCE"],
     input: 
         tsv = OUTDIR/f"{OUTPUT_NAME}.masked.prefiltered.tsv",
     output:

workflow/scripts/tsv_to_vcf.py

@@ -17,7 +17,7 @@ def tsv_to_vcf(tsv_file, vcf_file):
         # Process each row in the TSV file
         for index, row in tsv_df.iterrows():
             # Extract fields from the TSV row
-            chrom = 'NC_045512.2'
+            chrom = snakemake.params.ref_name
             pos = row['POS']
             ref = row['REF']
             alt = row['ALT']