Fix formatting

Former-commit-id: 87da1d3

Author: denis-yuen

seqware-distribution/docs/site/layouts/includes/workflow_conf.md

@@ -2,26 +2,25 @@
 Each workflow uses a simple INI file to record which variables it accepts,
 their types, and default values.  For example:
 
-<pre><code>#!ini
-# key=input_file:type=file:display=F:file_meta_type=text/plain
-input_file=${workflow_bundle_dir}/Workflow_Bundle_MyHelloWorld/${workflow-version}/data/input.txt
-# key=greeting:type=text:display=T:display_name=Greeting
-greeting=Testing
-
-cat=${workflow_bundle_dir}/Workflow_Bundle_MyHelloWorld/${workflow-version}/bin/gnu-coreutils-5.67/cat
-echo=${workflow_bundle_dir}/Workflow_Bundle_MyHelloWorld/${workflow-version}/bin/gnu-coreutils-5.67/echo
-
-# the output directory is a convention used in many workflows to specify a relative output path
-output_dir=seqware-results
-# the output_prefix is a convention used to specify the root of the absolute output path or an S3 bucket name 
-# you should pick a path that is available on all cluster nodes and can be written by your user
-output_prefix=./
-# manual output determines whether or not SeqWare should enforce the uniqueness of the final directory or not. 
-# If false, SeqWare places files in a directory specified by output_prefix/output_dir/workflowname_version/RANDOM/<files>
-# where RANDOM is an integer. If true, SeqWare places the files at output_prefix/output_dir and may overwrite existing
-# files
-manual_output=false
-</code></pre>
+	#!ini
+	# key=input_file:type=file:display=F:file_meta_type=text/plain
+	input_file=${workflow_bundle_dir}/Workflow_Bundle_MyHelloWorld/${workflow-version}/data/input.txt
+	# key=greeting:type=text:display=T:display_name=Greeting
+	greeting=Testing
+
+	cat=${workflow_bundle_dir}/Workflow_Bundle_MyHelloWorld/${workflow-version}/bin/gnu-coreutils-5.67/cat
+	echo=${workflow_bundle_dir}/Workflow_Bundle_MyHelloWorld/${workflow-version}/bin/gnu-coreutils-5.67/echo
+
+	# the output directory is a convention used in many workflows to specify a relative output path
+	output_dir=seqware-results
+	# the output_prefix is a convention used to specify the root of the absolute output path or an S3 bucket name 
+	# you should pick a path that is available on all cluster nodes and can be written by your user
+	output_prefix=./
+	# manual output determines whether or not SeqWare should enforce the uniqueness of the final directory or not. 
+	# If false, SeqWare places files in a directory specified by output_prefix/output_dir/workflowname_version/RANDOM/<files>
+	# where RANDOM is an integer. If true, SeqWare places the files at output_prefix/output_dir and may overwrite existing
+	# files
+	manual_output=false
 
 You access these variables in the Java workflow using the
 <tt>getProperty()</tt> method. When installing the workflow the ini file is