test input

README.md

@@ -1,8 +1,17 @@
 #### Usage
 $ open-choppy-env
-$ choppy install ...
+$ choppy install YaqingLiu/bcftools
 
-#### inputSamplesFile
-sample_id	tumor_fastq_1	tumor_fastq_2	normal_fastq_1	normal_fastq_1
-
-inputSamplesFile is in the form of tsv, and should be put into Aliyun OSS.
+#### Input File
+Input file should be in the form of json.
+For example:
+```
+{
+	"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"
+}
+```

inputs

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