cat

tasks/validation.wdl

@@ -66,16 +66,16 @@ task validation {
 		rtg vcfeval -b ${D5_10X} -c ${sample_name}.${tag}.mhc.vcf.gz -o ${sample_name}.${tag}.mhc -t ${sdf}	
 
 
-		cp ${sample_name}.${tag}.satellite/summary.txt > ${sample_name}.${tag}.satellite.summary.txt
-		cp ${sample_name}.${tag}.simple_repeat/summary.txt > ${sample_name}.${tag}.simple_repeat.summary.txt
-		cp ${sample_name}.${tag}.SINE/summary.txt > ${sample_name}.${tag}.SINE.summary.txt
-		cp ${sample_name}.${tag}.LINE/summary.txt > ${sample_name}.${tag}.LINE.summary.txt
-		cp ${sample_name}.${tag}.LTR/summary.txt > ${sample_name}.${tag}.LTR.summary.txt
-		cp ${sample_name}.${tag}.low_complexity/summary.txt > ${sample_name}.${tag}.low_complexity.summary.txt
-		cp ${sample_name}.${tag}.SD/summary.txt > ${sample_name}.${tag}.SD.summary.txt
-		cp ${sample_name}.${tag}.ins_breakpoint/summary.txt > ${sample_name}.${tag}.ins_breakpoint.summary.txt
-		cp ${sample_name}.${tag}.del_breakpoint/summary.txt > ${sample_name}.${tag}.del_breakpoint.summary.txt
-		cp ${sample_name}.${tag}.mhc/summary.txt > ${sample_name}.${tag}.mhc.summary.txt
+		cat ${sample_name}.${tag}.satellite/summary.txt > ${sample_name}.${tag}.satellite.summary.txt
+		cat ${sample_name}.${tag}.simple_repeat/summary.txt > ${sample_name}.${tag}.simple_repeat.summary.txt
+		cat ${sample_name}.${tag}.SINE/summary.txt > ${sample_name}.${tag}.SINE.summary.txt
+		cat ${sample_name}.${tag}.LINE/summary.txt > ${sample_name}.${tag}.LINE.summary.txt
+		cat ${sample_name}.${tag}.LTR/summary.txt > ${sample_name}.${tag}.LTR.summary.txt
+		cat ${sample_name}.${tag}.low_complexity/summary.txt > ${sample_name}.${tag}.low_complexity.summary.txt
+		cat ${sample_name}.${tag}.SD/summary.txt > ${sample_name}.${tag}.SD.summary.txt
+		cat ${sample_name}.${tag}.ins_breakpoint/summary.txt > ${sample_name}.${tag}.ins_breakpoint.summary.txt
+		cat ${sample_name}.${tag}.del_breakpoint/summary.txt > ${sample_name}.${tag}.del_breakpoint.summary.txt
+		cat ${sample_name}.${tag}.mhc/summary.txt > ${sample_name}.${tag}.mhc.summary.txt
 
 
 	>>>