diff --git a/tools/prodigal/Snakefile b/tools/prodigal/Snakefile
index b9da10936fff84bb505f64be0b1a2831d412f92a..b304adea1f7348077ed365d3741a143d33f6e2e9 100644
--- a/tools/prodigal/Snakefile
+++ b/tools/prodigal/Snakefile
@@ -23,20 +23,19 @@ Usage:  prodigal [-a trans_file] [-c] [-d nuc_file] [-f output_type]
          -v:  Print version number and exit.
 """
 
-__prodigal_exec_command = config.get(
-    'prodigal', {}
-).get('exec_command', 'prodigal')
+__prodigal_exec_command = config.get('prodigal', {}).get('exec_command', 'prodigal')
 __prodigal_modules = config.get('prodigal', {}).get('modules')
+__prodigal_options = config.get('prodigal', {}).get('options', '')
 
 rule prodigal:
     input:
         __prodigal_input
     output:
-        fasta_genes = __prodigal_fasta_genes
+        fasta_genes = __prodigal_fasta_genes,
         genes = __prodigal_genes
     params:
         exec_command = __prodigal_exec_command,
-        modules = __prodigal_modules
+        modules = __prodigal_modules,
         options = __prodigal_options
     run:
         command = []
diff --git a/tools/prodigal/example_usage/Snakefile b/tools/prodigal/example_usage/Snakefile
index 7861e9224c318e3b98f136196c42759e1e95e7bf..4b32331d84ec33fa11ea1b3299fcdbd9cfe12f3c 100644
--- a/tools/prodigal/example_usage/Snakefile
+++ b/tools/prodigal/example_usage/Snakefile
@@ -18,5 +18,5 @@ include: __prodigal_rules
 
 rule all:
     input:
-        fasta_genes = expand("{dir}/{{sample}}.fa".format(dir=__prodigal_output_dir), sample=SAMPLES)
+        fasta_genes = expand("{dir}/{{sample}}.fa".format(dir=__prodigal_output_dir), sample=SAMPLES),
         genes = expand("{dir}/{{sample}}.gbk".format(dir=__prodigal_output_dir), sample=SAMPLES)