bugfix: viloca

- typo fix
- all: depends on correct CSV

workflow/rules/common.smk

@@ -685,11 +685,16 @@ for srec in sample_list:
         # in adition to standard VCF files, ShoRAH2 also produces CSV tables
         if config.general["snv_caller"] == "shorah":
             results.append(os.path.join(sdir, "variants/SNVs/snvs.csv"))
+        elif config.general["snv_caller"] == "viloca":
+            results.append(os.path.join(sdir, "variants/SNVs/snv/cooccurring_mutations.csv"))
         # all snv callers ('shorah', 'lofreq') produce standard VCF files
         results.append(os.path.join(sdir, "variants/SNVs/snvs.vcf"))
     # local haplotypes
     if config.output["local"]:
-        results.append(os.path.join(sdir, "variants/SNVs/snvs.csv"))
+        if config.general["snv_caller"] == "shorah":
+            results.append(os.path.join(sdir, "variants/SNVs/snvs.csv"))
+        elif config.general["snv_caller"] == "viloca":
+            results.append(os.path.join(sdir, "variants/SNVs/snv/cooccurring_mutations.csv"))
     # global haplotypes
     if config.output["global"]:
         if config.general["haplotype_reconstruction"] == "savage":

workflow/rules/snv.smk

@@ -377,7 +377,7 @@ rule viloca:
 
         # Get absolute path for input files
         CWD=${{PWD}}
-        WORK_DIR="$(realpath -m {ouput.WORK_DIR})"
+        WORK_DIR="$(realpath -m {output.WORK_DIR})"
         BAM="$(realpath {input.BAM})"
         REF="$(realpath {input.REF})"
         OUTFILE="$(realpath -m {log.outfile})"