fix rules

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 = []

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)