Attempt to fix ht_stat

rules/Analysis/MGMT.rules

@@ -494,6 +494,22 @@ def analysis_plot_files_output():
                   "assembly_stats.html",
                   "assembly_stats.txt"], dir='%s/results' % AN_OUT)
 
+def analysis_stats_files_output():
+    return expand([
+                 '{dir}/{stat_flag}/{rtype}/cycle_composition_{n}.{ext}',
+                 '{dir}/{stat_flag}/{rtype}/cycle_quality_{n}.{ext}',
+                 '{dir}/{stat_flag}/{rtype}/cycle_quality_box_{n}.{ext}',
+                 '{dir}/{stat_flag}/{rtype}/info.tab',
+                 '{dir}/{stat_flag}/{rtype}/lane_tile_quality_{n}.{ext}',
+                 '{dir}/{stat_flag}/{rtype}/quality_QQ.{ext}',
+                 '{dir}/{stat_flag}/{rtype}/reads_length.{ext}',
+                 '{dir}/{stat_flag}/{rtype}/reads_quality.{ext}'],
+                 n = ['1', '2'],
+                 ext = ['gnuplot', 'png', 'tab'],
+                 dir = P_OUT,
+                 stat_flag = ['stats', 'stats_after_preprocessing'],
+                 rtype = ['MG', 'MT'])
+
 rule ANALYSIS_PLOT:
     log:
         AN_LOG

rules/Analysis/master.rules

@@ -42,22 +42,9 @@ def analysis_output_files():
                  #"results/MG.gene_kegg_krona.html",
                  #####################
                  "MGMT.vizbin.with-contig-names.points"], dir=AN_OUT)
-#    stats = expand([
-#                 '{dir}/{stat_flag}/{rtype}/cycle_composition_{n}.{ext}',
-#                 '{dir}/{stat_flag}/{rtype}/cycle_quality_{n}.{ext}',
-#                 '{dir}/{stat_flag}/{rtype}/cycle_quality_box_{n}.{ext}',
-#                 '{dir}/{stat_flag}/{rtype}/info.tab',
-#                 '{dir}/{stat_flag}/{rtype}/lane_tile_quality_{n}.{ext}',
-#                 '{dir}/{stat_flag}/{rtype}/quality_QQ.{ext}',
-#                 '{dir}/{stat_flag}/{rtype}/reads_length.{ext}',
-#                 '{dir}/{stat_flag}/{rtype}/reads_quality.{ext}'],
-#                 n=['1', '2'],
-#                 ext=['gnuplot', 'png', 'tab'],
-#                 dir=AN_OUT,
-#                 stat_flag=['stats', 'stats_after_preprocessing'],
-#                 rtype=['MG', 'MT'])
     plots = analysis_plot_files_output()
-    return all + plots # + stats
+    stats = analysis_stats_files_output()
+    return all + plots + stats
 
 # master command
 rule ANALYSIS: