cat

tasks/merge_mendelian_vote.wdl

@@ -11,9 +11,9 @@ task merge_mendelian_vote {
 
 		python /opt/merge_mendelian_vote.py ${mendelian_file} ${vote_file} ${mut_file} ${output_prefix}.mendelian.vote.txt
 
-		${output_prefix}.mendelian.vote.txt | awk '{ if ((length($6) < 51) || (length($7) < 51)) { print } }' > ${output_prefix}.snv
+		cat ${output_prefix}.mendelian.vote.txt | awk '{ if ((length($6) < 51) || (length($7) < 51)) { print } }' > ${output_prefix}.snv
 
-		${output_prefix}.mendelian.vote.txt | awk '{ if ((length($6) > 50) || (length($7) > 50)) { print } }' > ${output_prefix}.indel		
+		cat ${output_prefix}.mendelian.vote.txt | awk '{ if ((length($6) > 50) || (length($7) > 50)) { print } }' > ${output_prefix}.indel		
 
 	>>>