revised-bedtools-task

tasks/bedtools.wdl

 	command <<<
 	    set -e -o pipefail
 		bedtools multicov ${tmp_bam} -bed ${bed_file} > revread_count.txt 
-	
+
 	>>>
 
 	runtime {

workflow.wdl

 	scatter (sample in input_samples) {
 		call cp_bam.cp_bam as cp_bam {
 			input:
-			bam=sample[0],
-			bai=sample[1],
+			bam=sample[0]
 
 		}
 
 		call bedtools.bedtools as bedtools {
 			input:
-			bam=sample[0],
-			bai=sample[1],
+			bam=sample[0]
 			bed_file=bed_file
 
 		}