mv output dir to params

tools/strainphlan/sample2markers/Snakefile

@@ -8,11 +8,11 @@ rule sample2markers:
     input:
         __sample2markers_input
     output:
-        dir = __sample2markers_output_dir,
-        file = __sample2markers_output
+        __sample2markers_output
     params:
         exec_command = __sample2markers_exec_command,
         modules = __sample2markers_modules,
+        output_dir = __sample2markers_output_dir,
         options = __sample2markers_options
     threads:
         __sample2markers_threads
@@ -20,5 +20,5 @@ rule sample2markers:
         command = []
         if params.modules:
             command.append("module load {params.modules}")
-        command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {output.dir}")
+        command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {params.output_dir}")
         shell(" && ".join(command))