revised-bedtools-task

tasks/bedtools.wdl

 task bedtools {
 
-	File bam
-	File bai
+	Array[File] bam
+	Array[File] bai
 	File bed_file
 
 	String docker
 	String disk_size
 
 	command <<<
-		mkdir -p /cromwell_root/tmp/bedtools	
-		cp ${bam} ${bai} /cromwell_root/tmp/bedtools
-		cd /cromwell_root/tmp/bedtools
-		bedtools multicov -bams GCCACATA_S9_L001_R1_001.sorted.bam F1_S6_L001_R1_001.sorted.bam -bed ${bed_file} > revread_count.txt 
+	    set -e -o pipefail
+		cat ~{sep=" " bam}|bedtools multicov -bed ${bed_file} > revread_count.txt 
 	
 	>>>
 

workflow.wdl

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