summary

tasks/region.wdl

 
 		for i in *vcf.gz
 		do
-			cat $i | grep -v '#' >> ${sample}.${tag}.all.count.txt
-			cat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample}.${tag}.snv.mc.count.txt
-			cat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample}.${tag}.snv.mc.same.genotype.count.txt
-			cat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample}.${tag}.indel.mc.count.txt
-			cat $i | grep -v '#' | grep 'INDEL;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample}.${tag}.indel.mc.same.genotype.count.txt
+			cat $i | grep -v '#' >> ${sample_name}.${tag}.all.count.txt
+			cat $i | grep -v '#' | grep 'SNV;MC' | wc -l >> ${sample_name}.${tag}.snv.mc.count.txt
+			cat $i | grep -v '#' | grep 'SNV;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.snv.mc.same.genotype.count.txt
+			cat $i | grep -v '#' | grep 'INDEL;MC' | wc -l >> ${sample_name}.${tag}.indel.mc.count.txt
+			cat $i | grep -v '#' | grep 'INDEL;MC' | awk '{ if (($10 == $11) && ($11 == $12) && ($12 == $13)) { print } }' | wc -l >> ${sample_name}.${tag}.indel.mc.same.genotype.count.txt
 		done
 
 		ls *vcf.gz > file.list.txt
 		File ins_breakpoint_stat = "${sample_name}.${tag}.ins_breakpoint.vcfstat.txt"
 		File del_breakpoint_stat = "${sample_name}.${tag}.del_breakpoint.vcfstat.txt"
 		File mhc_stat = "${sample_name}.${tag}.mhc.vcfstat.txt"
-		File snv = "${sample}.${tag}.snv.mc.count.txt"
-		File snv_mc = "${sample}.${tag}.snv.mc.same.genotype.count.txt"
-		File indel = "${sample}.${tag}.indel.mc.count.txt"
-		File indel_mc = "${sample}.${tag}.indel.mc.same.genotype.count.txt"
+		File snv = "${sample_name}.${tag}.snv.mc.count.txt"
+		File snv_mc = "${sample_name}.${tag}.snv.mc.same.genotype.count.txt"
+		File indel = "${sample_name}.${tag}.indel.mc.count.txt"
+		File indel_mc = "${sample_name}.${tag}.indel.mc.same.genotype.count.txt"
 		File file_list = "file.list.txt"
-		File all = "${sample}.${tag}.all.count.txt"
+		File all = "${sample_name}.${tag}.all.count.txt"
 	}
 }