diff --git a/rules/gatk/Snakefile b/rules/gatk/Snakefile index e2c329c2..49e00a20 100644 --- a/rules/gatk/Snakefile +++ b/rules/gatk/Snakefile @@ -32,6 +32,7 @@ rule gatk_RealignerTargetCreator: "{params.knowns_settings}" " --out {output}" " 2>> {log}" + " && chmod -v g+w {output} 2>> {log}" # gatk_2015.sh GenomeAnalysisTK.jar -T RealignerTargetCreator -nt $(NUM_THREADS) -L $(EXOME_TRACK) -I $< -R $(REF) -known $(GATKRES_PATH_2k15)/Mills_and_1000G_gold_standard.indels.b37.vcf -known $(GATKRES_PATH_2k15)/1000G_phase1.indels.b37.vcf --out $@.tmp $(OUTPUT_TO_LOG) \ #MOUSE: gatk_2015.sh GenomeAnalysisTK.jar -T RealignerTargetCreator -nt $(NUM_THREADS) -L $(EXOME_TRACK) -I $< -R $(MOUSE_REF) -known /data/biotools/reference/mgp_indels/C57BL6NJ_CBAJDBA2.indels.vcf.gz --out $@.tmp $(OUTPUT_TO_LOG) \