上传文件至 ''

defaults

+ {
+        "ref_fasta":"GRCh38.d1.vd1.fa",
+        "ref_fasta_dir":"oss://hcc1395/reference_genome/GRCh38.d1.vd1",
+        "cluster_config":"OnDemand ecs.r6.xlarge img-ubuntu-vpc",
+        "disk_size":"600",
+        "docker_delly":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/delly:1.1.6"
+    }

inputs

+{
+"{{ project_name }}.sample_id": "{{ sample_id }}",
+"{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
+"{{ project_name }}.tumor_bam_bai": "{{ tumor_bam_bai }}",
+"{{ project_name }}.normal_bam": "{{ normal_bam }}",
+"{{ project_name }}.normal_bam_bai": "{{ normal_bam_bai }}",
+"{{ project_name }}.ref_fasta": "{{ ref_fasta }}",
+"{{ project_name }}.ref_fasta_dir": "{{ ref_fasta_dir }}",
+"{{ project_name }}.cluster_config": "{{cluster_config }}",
+"{{ project_name }}.disk_size": "{{ disk_size }}",
+"{{ project_name }}.docker_cnvkit": "{{ docker_cnvkit }}",
+"{{ project_name }}.sample_tsv": "{{ sample_tsv }}"
+}

workflow.wdl

+import "./tasks/delly.wdl" as delly
+
+workflow {{ project_name }}{
+    String sample_id
+    File ref_fasta_dir
+    String ref_fasta
+    File sample_tsv
+    File tumor_bam
+    File tumor_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String docker_delly
+    String cluster_config
+    String disk_size
+
+    call delly.delly as delly{
+        input:
+            sample=sample_id,
+            ref_dir=ref_fasta_dir,
+            fasta=ref_fasta,
+            sample_tsv=sample_tsv,
+            tumor_bam=tumor_bam,
+            tumor_bam_index=tumor_bam_bai,
+            normal_bam=normal_bam,
+            normal_bam_index=normal_bam_bai,
+            docker=docker_delly,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+
+    }
+}