add parameter: include dup

input_samples_file.tsv

-oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam	oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam.bai
-oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam	oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam.bai

inputs

 {
   "{{ project_name }}.input_bam_file": "{{ input_bam_file }}",
   "{{ project_name }}.input_bai_file": "{{ input_bai_file }}",
-  "{{ project_name }}.bed_file": "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", 
+  "{{ project_name }}.bed_file": "{{ bed_file }}", 
   "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
-  "{{ project_name }}.bedtools.disk_size": "{{disk_size}}"
+  "{{ project_name }}.bedtools.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.include_dup": "{{ include_dup }}"
 }

tasks/bedtools.wdl

 	Array[File] bam
 	Array[File] bai
 	File bed_file
-
+	
 	String docker
 	String cluster_config
 	String disk_size
+	Boolean include_dup
 
 	command <<<
 	    set -e -o pipefail
         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} > /bedtools/revread_count.txt
-
+		if ${include_dup}; then
+			bedtools multicov -D -bams ${sep=' ' bam} -bed ${bed_file} > /bedtools/revread_count.txt
+		else
+			bedtools multicov -bams ${sep=' ' bam} -bed ${bed_file} > /bedtools/revread_count.txt
+		fi
 	>>>
 
 	runtime {

workflow.wdl

 	File input_bam_file
 	File input_bai_file
 	File bed_file
+	Boolean include_dup
 	Array[File] bam = read_lines(input_bam_file)
 	Array[File] bai = read_lines(input_bai_file)
+	
 	call bedtools.bedtools as bedtools {
-			input:
-			bam=bam,
-			bai=bai,
-			bed_file=bed_file
+		input:
+		bam=bam,
+		bai=bai,
+		include_dup=include_dup,
+		bed_file=bed_file
 	}
 }