Update: README.md

README.md

@@ -1,4 +1,4 @@
-### Variant calling
+### Variant Calling
 This APP developed for somatic short variant discovery (SNVs + Indels).
 
 ***Supported callers***
@@ -13,24 +13,26 @@ Variant caller can be selected by setting `ture/false` in the submitted sample.c
 * WGS
 The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).
 
-
-### New version
+### New Releases
 * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
 * The `corealigner` step has been removed.
 
-### How to run this APP
+### Getting Started
 
 We recommend using choppy system and Aliyun OSS service. The command will look like this:
 
-```
+```Shell
+# Activate the choppy environment
 open-choppy-env
 
-choppy install YaqingLiu/variant-calling-latest
+# Install the APP
+choppy install YaqingLiu/variant-calling-latest [-f]
 
-choppy samples YaqingLiu/variant-calling-latest --no-default
-# sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2
+# List the parameters
+choppy samples YaqingLiu/variant-calling-latest [--no-default]
 
-choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project -l Label
+# Submit you task with the `samples.csv file` and `project name`
+choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label]
 
 # Query the status of all tasks in the project
 choppy query -L Label | grep "status"
@@ -38,6 +40,8 @@ choppy query -L Label | grep "status"
 
 **Please note**: The `defaults` can be forcibly replaced by the settings in `samples.csv`. Therefore, there is no need to contact me over this issue.
 
+The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2
+
 
 **Please carefully check**
 * the reference genome