revised-bedtools-task

tasks/bedtools.wdl

         mkdir -p /cromwell_root/tmp/bedtools
 		cp ${sep=' ' bai} /cromwell_root/tmp/bedtools
 		cd /cromwell_root/tmp/bedtools
-		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > revread_count.txt
+		bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > ~/revread_count.txt
 
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