MT assembly only rules

rules/Assembly/MGMT.rules

@@ -141,7 +141,6 @@ rule ASSEMBLY_MGMT_ASSEMBLY_1:
         rm -rf $TMPD
         """
 
-
 rule ASSEMBLY_MGMT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1:
     log:
         A_LOG
@@ -174,7 +173,6 @@ rule ASSEMBLY_MGMT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1:
         rm -rf $BUFFER* $TMP_FILE
         """
 
-
 rule ASSEMBLY_MGMT_ASSEMBLY_2:
     log:
         A_LOG

rules/Assembly/master.rules

@@ -3,7 +3,8 @@ A_OUT, A_LOG = prepare_environment('Assembly')
 
 # include sub rules
 include:
-    "MGMT.rules"
+    "MGMT.rules",
+    "MG.rules"
 
 def assembly_output_files():
     return expand('{dir}/{name}', name=[
@@ -24,3 +25,11 @@ rule ASSEMBLY_MT_ALL:
     shell:
         "echo 'MT Assembly Done'"
 
+# MG ASSEMBLY command
+# This will produce an MG-only assembly
+rule ASSEMBLY_MG_ALL:
+    input:
+        "%s/MG.assembly.merged.fa" % A_OUT
+    shell:
+        "echo 'MG Assembly Done'"
+