remove docker

README.md

@@ -1,6 +1,6 @@
 > Author: Jun Shang
 > Email: shangjunv@163.com
-> Last Updates: 23/11/2019
+> Last Updates: 22/10/2020
 
 #### Requirements
 
@@ -9,12 +9,12 @@
 
 ```
 $ source activate choppy
-$ choppy install junshang/cat-rename
+$ choppy install junshang/catreads
 $ choppy apps
 ```
 
 #### quick start
 
 ```
-$ choppy batch junshang/cat-rename-latest sample.csv --project-name Your_project_name
+$ choppy batch junshang/catreads-latest sample.csv --project-name Your_project_name
 ```

inputs

@@ -2,7 +2,6 @@
   "{{ project_name }}.fq1": "{{ fq1 }}",
   "{{ project_name }}.fq2": "{{ fq2 }}",
   "{{ project_name }}.fq3": "{{ fq3 }}",
-  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
 }

tasks/catreads.wdl

@@ -3,7 +3,6 @@ task catreads {
 	File fq2
 	String fq3
 	String disk_size
-	String docker
 	String cluster_config
 
 	command <<<
@@ -11,7 +10,6 @@ task catreads {
 	>>>
 
 	runtime {
-		docker: docker
 		systemDisk: "cloud_ssd 40"
 		cluster: cluster_config
 		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"

workflow.wdl

@@ -1,7 +1,6 @@
 import "./tasks/catreads.wdl" as catreads
 
 workflow {{ project_name }} {
-	String docker
 	String disk_size
 	File fq1
 	File fq2
@@ -13,7 +12,6 @@ workflow {{ project_name }} {
 			fq1=fq1,
 			fq2=fq2,
 			fq3=fq3,
-			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 	}