change resulting recalibration table files as temporary

Snakemake/IMAGE_calling/Snakefile

@@ -164,9 +164,7 @@ for prefix in all_files:
 for sample in all_samples:
     final_output_list.append("results/markduplicates/"+sample+".rg.sort.md.metrics")
     final_output_list.append("results/flagstat/"+sample+".flagstat")
-    final_output_list.append("results/gatk_recalibration/"+sample+".before.recal.table")
     final_output_list.append("results/gatk_recalibration/"+sample+".rg.sort.md.real.recal.bam")
-    final_output_list.append("results/gatk_recalibration/"+sample+".after.recal.table")
     final_output_list.append("results/gatk_recalibration/"+sample+"_recal_plots.pdf")
     final_output_list.append("results/qualimap/"+sample+"/qualimapReport.html")
     final_output_list.append("results/gatk_haplotypecaller/"+sample+".rg.sort.md.real.recal.g.vcf.gz")

Snakemake/IMAGE_calling/rules/recalibration.rules

@@ -15,7 +15,7 @@ rule BaseRecalibrator_1:
         known_variants=config["known_variants"]
         
     output:
-        protected("results/gatk_recalibration/{sample}.before.recal.table")
+        temp("results/gatk_recalibration/{sample}.before.recal.table")
         
     threads: config["BaseRecalibrator_1"]["cpu"]
     
@@ -61,7 +61,7 @@ rule BaseRecalibrator_2:
         recal_table="results/gatk_recalibration/{sample}.before.recal.table"
         
     output:
-        protected("results/gatk_recalibration/{sample}.after.recal.table")
+        temp("results/gatk_recalibration/{sample}.after.recal.table")
         
     threads: config["BaseRecalibrator_2"]["cpu"]