Update README.md

README.md

@@ -1,17 +1,28 @@
+***After generating all VCF files you want to include in the panel,***
+***you can use bcftools-merge to merge them into a single Panel of Normal VCF.***
 #### Usage
-$ open-choppy-env
-$ choppy install YaqingLiu/bcftools
-
+```shell
+# Enter the Choppy work environment
+open-choppy-env
+# APP `bcftools-merge` should be installed for the first time
+choppy install YaqingLiu/bcftools-merge
+# Create input file `samples.json`
+touch samples.json
+# Submit your job
+choppy batch YaqingLiu/bcftools-merge-latest samples.json -p project_name
+```
 #### Input File
-Input file should be in the form of json.
+Input file `samples.json` should be in the form of json.
 For example:
-```
+```json
 {
 	"vcf": [
           "oss://choppy-cromwell-result/test-choppy/..._pon.vcf",
           "oss://choppy-cromwell-result/test-choppy/..._pon.vcf",
           "oss://choppy-cromwell-result/test-choppy/..._pon.vcf"
         ],
-	"sample_id": "somatic_normal"
+	"panel_id": "PON_20200923",
+	"sample_id": "PON_20200923"
 }
-```
+```
+*PS: sample_id is necessary for Choppy system*

inputs

@@ -1,6 +1,7 @@
 {
+  "{{ project_name }}.vcf": {{ vcf | tojson }},
+  "{{ project_name }}.panel_id": {{ panel_id }}
   "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
-  "{{ project_name }}.vcf": {{ vcf | tojson  }},
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}"
 }

tasks/bcftools.wdl

@@ -1,6 +1,7 @@
 task bcftools {
 
 	Array[File] vcf
+	String panel_id
 	String docker
 	String cluster_config
 	String disk_size
@@ -16,7 +17,7 @@ task bcftools {
 			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
 		done
 
-		bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
+		bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf
 	>>>
 
 	runtime {
@@ -27,6 +28,6 @@ task bcftools {
 	}
 	
 	output {
-		File panel_of_normal_vcf = "panel_of_normal.vcf"
+		File panel_of_normal_vcf = "${panel_id}_pon.vcf"
 	}
 }

workflow.wdl

@@ -6,10 +6,12 @@ workflow {{ project_name }} {
 	String disk_size
 	String cluster_config
 	Array[File] vcf
+	String panel_id
 
 	call bcftools.bcftools as bcftools {
 		input:
 		vcf=vcf,
+		panel_id=panel_id,
 		docker=bcftools_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config