添加 'tasks/TNseq_1.wdl'

tasks/TNseq_1.wdl

@@ -0,0 +1,54 @@
+task sentieon_TNseq{
+    String sample_id
+    File tumor_bam
+    File tumor_bam_bai
+    File? normal_bam
+    File? normal_bam_bai
+    String tumor_name
+    String normal_name
+
+    File ref_dir
+    String ref_fasta
+    File germline_resource
+    File germline_resource_tbi
+    File? regions
+    Int? interval_padding
+
+    # excute env
+    String docker
+    String cluster_config
+    String disk_size
+    String SENTIEON_LICENSE
+
+
+    command <<<
+        set -o pipefail
+        set -exo
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(nproc)
+        
+        sentieon licclnt ping -s 172.25.2.5:8990 && echo 'It works.'
+
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+    }
+
+    output{
+        File raw_vcf = "${sample_id}.TNseq.raw.vcf"
+        File raw_vcf_index = "${sample_id}.TNseq.raw.vcf.idx"
+        File vcf = "${sample_id}.bwa_TNseq.vcf"
+        File vcf_index = "${sample_id}.bwa_TNseq.vcf.idx"
+        File contamination = "${sample_id}.contamination"
+        File contamination_segments = "${sample_id}.contamination.segments"
+        File orientation = "${sample_id}.orientation"
+
+
+    }
+}