align

inputs

 {
-  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/milaboratory/mixcr:latest",
   "{{ project_name }}.sample": "{{ sample_name }}",
-  "{{ project_name }}.tumor_fastq_2": "{{ tumor_fastq_2 }}",
-  "{{ project_name }}.tumor_fastq_1": "{{ tumor_fastq_1 }}",
+  "{{ project_name }}.read1": "{{ read1 }}",
+  "{{ project_name }}.read2": "{{ read2 }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}"
 }

workflow.wdl

+import "./tasks/align.wdl" as align
+
+workflow {{ project_name }} {
+
+	File read1
+	File read2
+	
+	
+	call align.align as align {
+		input: read1=read1, read2=read2
+	}
+        	
+}