add file removing on success

Snakefile

@@ -206,7 +206,7 @@ if config["star_mapping"]["do"]:
         
     #first pass mapping
     star_mapping_pass1_input = adapters_output
-    star_mapping_pass1_index = star_index_output_done
+    star_mapping_pass1_index = star_index_output_dir
     star_mapping_pass1_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}_init.out"
     star_mapping_pass1_output_prefix =  "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_init_"
     star_mapping_pass1_junctions = "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_init_SJ.out.tab"
@@ -217,7 +217,7 @@ if config["star_mapping"]["do"]:
     
     #Second pass mapping
     star_mapping_pass2_input = adapters_output
-    star_mapping_pass2_index = star_index_output_done
+    star_mapping_pass2_index = star_index_output_dir
     star_mapping_pass2_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}.out"
     star_mapping_pass2_output_prefix =  "02-Mapping/STAR/{REF}/{SAMPLE}_{REF}_"
     star_mapping_pass2_junctions = expand("02-Mapping/STAR/{{REF}}/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples)
@@ -313,10 +313,19 @@ rule rnaflow:
         
 
 onsuccess:
-    # copy metrics json in the corresponding multiQC output when you are in exploratory mode
+    # remove file from first star mapping
+    import os
+    import glob
     import shutil
+    for file in glob.glob('02-Mapping/STAR/*/*init*'):
+        if os.path.isfile(file):
+            os.remove(file)
+        elif os.remove.isdir(file):
+            shutil.rmtree(file)
+        else:    
+            print("Error: %s file not found" % file)
+
     # move cluster log files
-    import os
     pattern = re.compile("slurm.*")
     dest = "cluster_logs"
     for filepath in os.listdir("."):

workflow/rules/star_mapping_pass1.rules

@@ -27,8 +27,8 @@ rule star_mapping_pass1:
         fastq = star_mapping_pass1_input,
         index = star_mapping_pass1_index
     output:
-        jontion = star_mapping_pass1_junctions,
-        bam = star_mapping_pass1_bam
+        jontion = temp(star_mapping_pass1_junctions),
+        bam = temp(star_mapping_pass1_bam)
     params:
         prefix = temp(star_mapping_pass1_output_prefix),
         #read_groups = star_mapping_pass1_read_groups,