fix bug: input

README.md

@@ -5,17 +5,43 @@
 > E-mail：yaqing.liu@outlook.com
 >
 
-## 安装指南
+## Install
 
 ```
-# 激活choppy环境
+# activate choppy environment
 open-choppy-env
-# 安装app
+# install app
 choppy install YaqingLiu/CNVkit
 ```
 
 ## Copy number calling pipeline
 ![image](https://cnvkit.readthedocs.io/en/stable/_images/workflow.png)
 
-
-## App输入文件
+## Input
+```json
+{
+	"tumor_bam": [
+          "oss://choppy-cromwell-result/...bam",
+          "oss://choppy-cromwell-result/...bam",
+          "oss://choppy-cromwell-result/...bam"
+	],
+	"tumor_bai": [
+          "oss://choppy-cromwell-result/...bai",
+          "oss://choppy-cromwell-result/...bai",
+          "oss://choppy-cromwell-result/...bai"
+	],
+	"normal_bam": [
+          "oss://choppy-cromwell-result/...bam",
+          "oss://choppy-cromwell-result/...bam",
+          "oss://choppy-cromwell-result/...bam"
+	],
+	"normal_bai": [
+          "oss://choppy-cromwell-result/...bai",
+          "oss://choppy-cromwell-result/...bai",
+          "oss://choppy-cromwell-result/...bai"
+    ],
+	"sample_id": "..."
+}
+```
+#### Output
+A segment file and some intermediate *.cnn/cns will be generated, and the segment file can be imported into IGV.

tasks/access.wdl

@@ -19,4 +19,4 @@ task access {
     output {
         File access_bed = "access-5kb-mappable.hg38.bed"
     }
-}
+}

tasks/batch.wdl

@@ -4,7 +4,7 @@ task batch {
     Array[File] tumor_bai
     Array[File] normal_bam
     Array[File] normal_bai
-    String bed
+    File bed
     File ref_dir
     String fasta
     File access_bed
@@ -38,7 +38,4 @@ task batch {
         File reference_cnn = "my_reference.cnn"
         Array[File] result = glob("result/*")
     }
-}
-
-
-
+}

workflow.wdl

@@ -8,7 +8,7 @@ workflow {{ project_name }} {
     Array[File] tumor_bai
     Array[File] normal_bam
     Array[File] normal_bai
-    String bed
+    File bed
     File ref_dir
     String fasta
 	String docker