diff --git a/bio/gridss/assemble/test/Snakefile b/bio/gridss/assemble/test/Snakefile
index 81e0b786a13..91942735f2c 100644
--- a/bio/gridss/assemble/test/Snakefile
+++ b/bio/gridss/assemble/test/Snakefile
@@ -33,8 +33,8 @@ reference_index_endings = (".amb",".ann", ".bwt", ".pac", ".sa", ".gridsscache",
 
 rule gridss_assemble:
     input:
-        bams=expand("mapped/{sample}.bam", sample=samples),
-        bais=expand("mapped/{sample}.bam.bai", sample=samples),
+        bam=expand("mapped/{sample}.bam", sample=samples),
+        bai=expand("mapped/{sample}.bam.bai", sample=samples),
         reference="reference/genome.fasta",
         dictionary="reference/genome.dict",
         indices=multiext("reference/genome.fasta", *reference_index_endings),
diff --git a/bio/gridss/assemble/test/reference/genome.dict b/bio/gridss/assemble/test/reference/genome.fasta.dict
similarity index 100%
rename from bio/gridss/assemble/test/reference/genome.dict
rename to bio/gridss/assemble/test/reference/genome.fasta.dict
diff --git a/bio/gridss/assemble/wrapper.py b/bio/gridss/assemble/wrapper.py
index be5002ac0b2..5ae52f75e0b 100644
--- a/bio/gridss/assemble/wrapper.py
+++ b/bio/gridss/assemble/wrapper.py
@@ -31,12 +31,10 @@
             )
         )
 
-dictionary = path.splitext(reference)[0] + ".dict"
+dictionary = reference + ".dict"
 if not path.exists(dictionary):
     raise ValueError(
-        "{dictionary}.dict missing. Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard".format(
-            dictionary=dictionary
-        )
+        f"{dictionary} missing. Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard."
     )
 
 shell(
@@ -45,6 +43,6 @@
     "--threads {snakemake.threads} "  # Threads
     "--workingdir {snakemake.params.workingdir} "  # Working directory
     "--assembly {snakemake.output.assembly} "  # Assembly output
-    "{snakemake.input.bams} "
+    "{snakemake.input.bam} "
     "{extra}) {log}"
 )
diff --git a/bio/gridss/call/test/reference/genome.dict b/bio/gridss/call/test/reference/genome.fasta.dict
similarity index 100%
rename from bio/gridss/call/test/reference/genome.dict
rename to bio/gridss/call/test/reference/genome.fasta.dict
diff --git a/bio/gridss/call/wrapper.py b/bio/gridss/call/wrapper.py
index b07ef205d66..7b38ed22081 100644
--- a/bio/gridss/call/wrapper.py
+++ b/bio/gridss/call/wrapper.py
@@ -31,12 +31,10 @@
             )
         )
 
-dictionary = path.splitext(reference)[0] + ".dict"
+#dictionary = path.splitext(reference)[0] + ".dict"
 if not path.exists(dictionary):
     raise ValueError(
-        "{dictionary}.dict missing. Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard".format(
-            dictionary=dictionary
-        )
+        f"{dictionary} missing. Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard."
     )
 
 shell(
diff --git a/bio/gridss/preprocess/test/reference/genome.dict b/bio/gridss/preprocess/test/reference/genome.fasta.dict
similarity index 100%
rename from bio/gridss/preprocess/test/reference/genome.dict
rename to bio/gridss/preprocess/test/reference/genome.fasta.dict
diff --git a/bio/gridss/preprocess/wrapper.py b/bio/gridss/preprocess/wrapper.py
index e60cb5232f6..7e944846c93 100644
--- a/bio/gridss/preprocess/wrapper.py
+++ b/bio/gridss/preprocess/wrapper.py
@@ -31,12 +31,10 @@
             )
         )
 
-dictionary = path.splitext(reference)[0] + ".dict"
+# dictionary = path.splitext(reference)[0] + ".dict" --> leads to incorrect paths (reference.dict), which is incompatible with setup reference (reference.fa.dict)
 if not path.exists(dictionary):
     raise ValueError(
-        "{dictionary}.dict missing. Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard".format(
-            dictionary=dictionary
-        )
+        f"{dictionary} missing or wrong naming (reference.fa.dict). Please make sure the reference dictionary was properly created. This can be accomplished for example by CreateSequenceDictionary.jar from Picard."
     )
 
 shell(