diff --git a/snakePipes/snakePipes.py b/snakePipes/snakePipes.py
index 63b49f6d1..6d358a5fa 100755
--- a/snakePipes/snakePipes.py
+++ b/snakePipes/snakePipes.py
@@ -103,6 +103,12 @@ def parse_arguments():
         "in the workflow-specific yaml files and where conda is installed.",
     )
 
+    configParser.add_argument(
+        "--snakemakeProfile",
+        help="Path to custom snakemake profile file.",
+        default=defaults["snakemakeProfile"]
+    )
+
     configParser.add_argument(
         "--organismsDir",
         help="The directory where global organism YAML files are to be stored. Both "
@@ -381,6 +387,7 @@ def updateConfig(args):
     if args.configMode == "manual":
         d = {
             "snakemakeOptions": args.snakemakeOptions,
+            "snakemakeProfile": args.snakemakeProfile,
             "condaEnvDir": args.condaEnvDir,
             "organismsDir": args.organismsDir,
             "tempDir": args.tempDir,
@@ -407,6 +414,16 @@ def updateConfig(args):
             sys.exit("Config file not found\n")
     updatedDict = cof.merge_dicts(currentDict, d)
     cof.write_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), updatedDict)
+
+    #update conda-prefix in snakemakeProfile
+    if args.condaEnvDir:
+        profilePath = cof.resolveSnakemakeProfile(d['snakemakeProfile'], baseDir)
+        f = open(profilePath / 'config.yaml')
+        pf = yaml.load(f, Loader=yaml.FullLoader)
+        pf['conda-prefix'] = args.condaEnvDir
+        cof.write_configfile(os.path.join(profilePath, "config.yaml"), pf)
+        f.close()
+
     cof.load_configfile(
         os.path.join(baseDir, "shared", "defaults.yaml"), True, "Final Updated Config"
     )
diff --git a/snakePipes/workflows/DNAmapping/Snakefile b/snakePipes/workflows/DNAmapping/Snakefile
index 579d10430..f5047efc3 100755
--- a/snakePipes/workflows/DNAmapping/Snakefile
+++ b/snakePipes/workflows/DNAmapping/Snakefile
@@ -63,7 +63,7 @@ if "allelic-mapping" in mode:
             SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome_alias + ".txt.gz"
         elif len(strains) == 2:
             allele_hybrid = 'dual'
-            SNPFile = SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt"
+            SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt"
 
         include: os.path.join(maindir, "shared", "rules", "masked_genomeIndex.snakefile")
     elif allele_mode == 'map_only':
diff --git a/snakePipes/workflows/mRNAseq/Snakefile b/snakePipes/workflows/mRNAseq/Snakefile
index 9a914a587..d551b0f4b 100755
--- a/snakePipes/workflows/mRNAseq/Snakefile
+++ b/snakePipes/workflows/mRNAseq/Snakefile
@@ -52,15 +52,16 @@ if not fromBAM:
 
     ## Allele-specific JOBS
     if "allelic-mapping" in mode:
+        genome_alias = os.path.splitext(os.path.basename(genome))[0]
         # Updated global vars if mode = "allelic-mapping"
         if allele_mode == 'create_and_map':
             star_index_allelic = 'snp_genome/star_Nmasked/Genome'
             if len(strains) == 1:
                 allele_hybrid = 'single'
-                SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome + ".txt.gz"
+                SNPFile = "snp_genome/all_SNPs_" + strains[0] + "_" + genome_alias + ".txt.gz"
             elif len(strains) == 2:
                 allele_hybrid = 'dual'
-                SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome + ".txt"
+                SNPFile = "snp_genome/all_" + strains[1] + "_SNPs_" + strains[0] + "_reference.based_on_" + genome_alias + ".txt"
 
             include: os.path.join(maindir, "shared", "rules", "masked_genomeIndex.snakefile")
         elif allele_mode == 'map_only':