添加 'workflow.wdl'

workflow.wdl

@@ -0,0 +1,49 @@
+import "./tasks/TNscope.wdl" as TNscope
+
+workflow {{ project_name }} {
+    String sample_id
+    File tumor_bam
+    File tumor_bam_bai
+    File? normal_bam
+    File? normal_bam_bai
+    String tumor_name
+    String normal_name
+    File tumor_recall_data
+    File normal_recall_data
+
+    File ref_dir
+    String ref_fasta
+    File dbsnp_dir
+    String dbsnp
+
+    # excute env
+    String docker_sentieon
+    String cluster_config
+    String disk_size
+    String SENTIEON_LICENSE
+
+    call TNscope.sentieon_TNscope as sentieon_TNscope{
+        input:
+            sample_id=sample_id,
+            tumor_bam=tumor_bam,
+            tumor_bam_bai=tumor_bam_bai,
+            normal_bam=normal_bam,
+            normal_bam_bai=normal_bam_bai,
+            tumor_name=sample_id+'_T',
+            normal_name=sample_id+'_N',
+            tumor_recall_data=tumor_recall_data,
+            normal_recall_data=normal_recall_data,
+            ref_dir=ref_dir,
+            ref_fasta=ref_fasta,
+            dbsnp_dir=dbsnp_dir,
+            dbsnp=dbsnp,
+            docker=docker_sentieon,
+            cluster_config=cluster_config,
+            disk_size=disk_size,
+            SENTIEON_LICENSE=SENTIEON_LICENSE
+
+
+    }
+
+
+}