add options

defaults

     "fa": "GRCh38.d1.vd1.fa",
     "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
     "disk_size": "200",
-	"docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
-    "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc"
+    "docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
+    "cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+    "min_base_quality": "0",
+    "min_mapping_quality": "0"
 }

inputs

   "{{ project_name }}.docker": "{{ docker }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}",
   "{{ project_name }}.fa": "{{ fa }}",
-  "{{ project_name }}.fai": "{{ fai }}",
   "{{ project_name }}.bed": "{{ bed }}",
   "{{ project_name }}.bam": "{{ bam }}",
   "{{ project_name }}.bai": "{{ bai }}",
+  "{{ project_name }}.min_mapping_quality": "{{ min_mapping_quality }}",
+  "{{ project_name }}.min_base_quality": "{{ min_base_quality }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
   "{{ project_name }}.sample_id": "{{ sample_id }}"

tasks/BAMReadCount.wdl

 task BAMReadCount {
 
-	String sample_id
-	File ref_dir
-	String fa
-	File fai
-	File bed
-	File bam
-	File bai
-	String docker
-	String cluster_config
-	String disk_size
+    String sample_id
+    File ref_dir
+    String fa
+    File bed
+    File bam
+    File bai
+    String min_mapping_quality
+    String min_base_quality
+    String docker
+    String cluster_config
+    String disk_size
 
-	command <<<
-		bam-readcount -w 0 -q1 -f ${ref_dir}/${fa} -l ${bed} ${bam} > ${sample_id}.readcount
-	>>>
+    command <<<
+        bam-readcount -w 0 -q ${min_mapping_quality} -b ${min_base_quality} -f ${ref_dir}/${fa} -l ${bed} ${bam} > ${sample_id}.readcount
+    >>>
 
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
+    runtime {
+        docker: docker
+        cluster: cluster_config
+        systemDisk: "cloud_ssd 40"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
 
-	output {
-		File BAMReadCount = "${sample_id}.readcount"
-	}
+    output {
+        File BAMReadCount = "${sample_id}.readcount"
+    }
 }

workflow.wdl

 import "./tasks/BAMReadCount.wdl" as BAMReadCount
 
 workflow {{ project_name }} {
-	File ref_dir
-	String fa
-	File fai
-	File bed
-	File bam
-	File bai
-	String sample_id
-	String docker
-	String cluster_config
-	String disk_size
-	
+    File ref_dir
+    String fa
+    File bed
+    File bam
+    File bai
+    String min_mapping_quality
+    String min_base_quality
+    String sample_id
+    String docker
+    String cluster_config
+    String disk_size
+    
 
-	call BAMReadCount.BAMReadCount as BAMReadCount {
-		input:
-		ref_dir=ref_dir,
-		fa=fa,
-		fai=fai,
-		bed=bed,
-		bam=bam,
-		bai=bai,
-		docker=docker,
-		disk_size=disk_size,
-		cluster_config=cluster_config,
-		sample_id=sample_id
-	}
+    call BAMReadCount.BAMReadCount as BAMReadCount {
+        input:
+        ref_dir=ref_dir,
+        fa=fa,
+        fai=fai,
+        bed=bed,
+        bam=bam,
+        bai=bai,
+        min_mapping_quality=min_mapping_quality,
+        min_base_quality=min_base_quality,
+        docker=docker,
+        disk_size=disk_size,
+        cluster_config=cluster_config,
+        sample_id=sample_id
+    }
 }