IMAGE_vqsr : add script dir in PATH to execute filter_multi_samples_vcf.py

Snakemake/IMAGE_vqsr/Snakefile

 ##########################################################
 ### Import section
 import yaml
-import os
+import os,sys
 import collections
 ##########################################################
 ### system options
@@ -35,7 +35,8 @@ for rule in rule_resources:
 
 # add tabix and filter_multi_sample_vcf.py in PATH
 tabix_dir=os.path.dirname(config['bin']['tabix'])
-script_dir=os.path.abspath('script')
+snakefile_path=sys.argv[sys.argv.index("-s") +1] if "-s" in sys.argv else "./Snakefile"
+script_dir=os.path.join(os.path.abspath(os.path.dirname(snakefile_path)),'script')
 os.environ['PATH'] = tabix_dir + os.pathsep + script_dir + os.pathsep + os.environ['PATH']
 
 ##########################################################
@@ -81,10 +82,12 @@ final_outputs.append("results/split_SNP_INDEL/VQSR_trainingSet_untrusted_uniquel
 # common hard filtered SNP and INDEL 
 final_outputs.append("results/hard_filtering/VQSR_trainingSet_trusted_3callers_hardFiltered_variants_SNP.vcf.gz")
 final_outputs.append("results/hard_filtering/VQSR_trainingSet_trusted_3callers_hardFiltered_variants_INDEL.vcf.gz")
+
 # Final recalibrated GATK SNP and INDEL
 gatk_prefix = os.path.splitext(os.path.basename(config['GATK_variants']))[0]
 if gatk_prefix.endswith('vcf') :
 	gatk_prefix = os.path.splitext(gatk_prefix)[0]
+
 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")
@@ -126,6 +129,6 @@ onsuccess:
     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)
-        os.remove(f)
+    #~ for f in temp_list:
+        #~ print(f)
+        #~ os.remove(f)