IMAGE_vqsr : add bcftools stat output in final output list and define final temp file to remove

Snakemake/IMAGE_vqsr/Snakefile

@@ -89,9 +89,8 @@ final_outputs.append("results/VQSR/" + gatk_prefix +"_vqsr_SNP.vcf.gz")
 final_outputs.append("results/VQSR/" + gatk_prefix +"_vqsr_INDEL.vcf.gz")
 final_outputs.append("results/genoFilter/" + gatk_prefix +"_vqsr_SNP_genFiltered.vcf.gz")
 final_outputs.append("results/genoFilter/" + gatk_prefix +"_vqsr_INDEL_genFiltered.vcf.gz")
-final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_SNP_genFiltered.stat")
-final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_INDEL_genFiltered.stat")
-
+final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_SNP_genFiltered.stats")
+final_outputs.append("results/bcftools_stats/" + gatk_prefix +"_vqsr_INDEL_genFiltered.stats")
 #~ print(final_outputs)
 
 rule all:
@@ -103,17 +102,29 @@ onsuccess:
   if not "--notemp" in sys.argv :
     temp_list = list()
     print("remove remained temporary file :\n")
+    
+    # uniq variants
+    for caller in ["gatk","freebayes","mpileup"] :
+        temp_list.append("results/intersect/uniq_"+caller+"_variants.vcf.gz.tbi")
+    temp_list.append("results/intersect/VQSR_trainingSet_untrusted_uniquely_called_variants.vcf.gz.tbi")
+    
+    # common variants
+    temp_list.append('results/intersect/common_variants.vcf.gz.tbi')
+    temp_list.append('results/hard_filtering/common_SNP_tagged.vcf.gz.tbi')
+    temp_list.append('results/hard_filtering/common_INDEL_tagged.vcf.gz.tbi')
+    
     # splited VCF files, except for uniquely called training set
     for prefix in trainingSets:
         if prefix != 'VQSR_trainingSet_trusted_3callers_hardFiltered_variants' and prefix != 'VQSR_trainingSet_untrusted_uniquely_called_variants': 
             temp_list.append("results/split_SNP_INDEL/" + prefix + "_SNP.vcf.gz")
             temp_list.append("results/split_SNP_INDEL/" + prefix + "_INDEL.vcf.gz")
-            #temp_list.append("results/split_SNP_INDEL/" + prefix + "_SNP.vcf.gz.tbi")
-            #temp_list.append("results/split_SNP_INDEL/" + prefix + "_INDEL.vcf.gz.tbi")
+            temp_list.append("results/split_SNP_INDEL/" + prefix + "_SNP.vcf.gz.tbi")
+            temp_list.append("results/split_SNP_INDEL/" + prefix + "_INDEL.vcf.gz.tbi")
+    
     temp_list.append('results/split_SNP_INDEL/common_SNP.vcf.gz')
     temp_list.append('results/split_SNP_INDEL/common_INDEL.vcf.gz')
-    #temp_list.append('results/split_SNP_INDEL/common_SNP.vcf.gz.tbi')
-    #temp_list.append('results/split_SNP_INDEL/common_INDEL.vcf.gz.tbi')
+    temp_list.append('results/split_SNP_INDEL/common_SNP.vcf.gz.tbi')
+    temp_list.append('results/split_SNP_INDEL/common_INDEL.vcf.gz.tbi')
 
     for f in temp_list:
         print(f)