Update README.md

README.md

@@ -17,9 +17,8 @@ open-choppy-env
 choppy install YaqingLiu/CNVkit
 ```
 
-## Copy number calling pipeline
-![image](https://cnvkit.readthedocs.io/en/stable/_images/workflow.png)
 ## Input
+Please note that the input file of this APP is in the JSON format instead of CSV.
 ```json
 {
     "tumor_bam": [
@@ -47,7 +46,16 @@ choppy install YaqingLiu/CNVkit
     "reference": "..." # this parameter is optional
 }
 ```
-## Note
+
+## Submit your task
+```
+# choppy batch
+chopppy batch YaqingLiu/CNVkit-latest samples.json -p project_name
+```
+
+## Copy number calling pipeline
+![image](https://cnvkit.readthedocs.io/en/stable/_images/workflow.png)
+### Note
 <font color=darkred>***-m {hybrid,amplicon,wgs}, --seq-method {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}***</font>
 
 Sequencing assay type: hybridization capture ('hybrid'), targeted amplicon sequencing ('amplicon'), or whole genome sequencing ('wgs').