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",
+        "ref_flat":"oss://hcc1395/reference_genome/GRCh38.d1.vd1/refFlat.txt",
+        "docker_cnvkit":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/cnvkit:0.9.6a0"
+
+    }

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 }}.ref_flat": "{{ ref_flat }}"
+}

workflow.wdl

+version 1.0
+import "./tasks/CNVkit.wdl" as cnvkit
+
+workflow {{ project_name }} {
+    String sample_id
+    File ref_fasta_dir
+    String ref_fasta
+    File ref_flat
+    File tumor_bam
+    File tumor_bam_bai
+    File? normal_bam
+    File? normal_bam_bai
+    String docker_cnvkit
+    String cluster_config
+    String disk_size
+
+    call cnvkit.cnvkit as cnvkit{
+        input:
+            sample=sample_id,
+            ref_dir=ref_fasta_dir,
+            fasta=ref_fasta,
+            ref_flat=ref_flat,
+            tumor_bam=tumor_bam,
+            tumor_bam_index=tumor_bam_bai,
+            normal_bam=normal_bam,
+            normal_bam_index=normal_bam_bai,
+            docker=docker_cnvkit,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+    }
+
+
+}