上传文件至 ''

defaults

+{
+       "tumour_bam":"",
+       "tumour_bam_bai":"",
+        "normal_bam":"",
+        "normal_bam_bai":"",
+        "ref_fasta":"GRCh38.d1.vd1.fa",
+        "ref_dir":"oss://hcc1395/reference_genome/GRCh38.d1.vd1",
+        "sample_id":"",
+        "docker":"registry.cn-shanghai.aliyuncs.com/hcc1395_aliyun/strelka:v2.9.10",
+        "cluster_config":"OnDemand ecs.sn1ne.4xlarge img-ubuntu-vpc",
+        "disk_size":"500"
+}

inputs

+{
+    "{{ project_name }}.tumour_bam": "{{ tumour_bam }}",
+    "{{ project_name }}.tumour_bam_bai": "{{ tumour_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_dir": "{{ ref_dir }}",
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
+    "{{ project_name }}.manta_indel_vcf": "{{ manta_indel_vcf }}",
+    "{{ project_name }}.manta_indel_vcf_index": "{{ manta_indel_vcf_index }}",
+    "{{ project_name }}.docker_stralka": "{{ docker_stralka }}",
+    "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+    "{{ project_name }}.disk_size": "{{ disk_size }}"
+
+}

workflow.wdl

+import "./tasks/stralka.wdl" as stralka
+
+workflow {{ project_name }} {
+    File tumour_bam
+    File tumour_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String ref_fasta
+    File ref_dir
+    String sample_id
+    File? manta_indel_vcf
+    File? manta_indel_vcf_index
+    
+    # excute env
+    String docker_stralka
+    String cluster_config
+    String disk_size
+
+    call stralka.strelka_calling as stralka{
+        input:
+            tumour_bam=tumour_bam,
+            tumour_bam_bai=tumour_bam_bai,
+            normal_bam=normal_bam,
+            normal_bam_bai=normal_bam_bai,
+            ref_fasta=ref_fasta,
+            ref_dir=ref_dir,
+            sample_id=sample_id,
+            docker=docker_stralka,
+            cluster_config=cluster_config,
+            disk_size=disk_size
+    }
+
+}