added trie serialization step

rewrite-taxonomy.snakefile

@@ -5,19 +5,23 @@ rule all:
     input:
         config['OUTDIR'] + '/finish.txt',
         config['OUTDIR'] + '/taxid_microorganisms.txt',
-        config['OUTDIR'] + '/taxa+id_microorganisms.txt'
+        config['OUTDIR'] + '/taxa+id_microorganisms.txt',
+        config['OUTDIR'] + '/taxa+id_microorganisms.trie',
+        config['OUTDIR'] + '/taxid_full.txt',
+        config['OUTDIR'] + '/taxa+id_full.txt',
+        config['OUTDIR'] + '/taxa+id_full.trie'
 
 
 rule check:
     input:
-        config['OUTDIR'] + '/taxa+id_microorganisms.txt'
+        config['OUTDIR'] + '/taxa+id_{root}.txt'
 
     output:
-        config['OUTDIR'] + '/finish.txt'
+        config['OUTDIR'] + '/taxa+id_{root}.trie'
 
 
     shell:
-        '''{config[ALVISNLP]} -J-Xmx12G -alias taxo {input} -alias finish {output} check-taxonomy.plan'''
+        '''{config[ALVISNLP]} -J-Xmx12G -alias taxo {input} -alias trie {output} compile-taxonomy.plan'''
 
 
 rule microorganisms: