添加 'tasks/TNscope.wdl'

tasks/TNscope.wdl

@@ -0,0 +1,53 @@
+task sentieon_TNscope{
+    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
+    String cluster_config
+    String disk_size
+    String SENTIEON_LICENSE
+
+
+    command <<<
+        set -o pipefail
+        set -exo
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(nproc)
+
+        sentieon driver -t $nt -r ${ref_dir}/${ref_fasta} \
+        -i ${tumor_bam} -q ${tumor_recall_data} \
+        -i ${normal_bam} -q ${normal_recall_data} \
+        --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
+        --disable_detector sv --trim_soft_clip \
+        --dbsnp ${dbsnp_dir}/${dbsnp} ${sample_id}.TNscope.vcf || { echo "TNscope failed"; exit 1; }
+        
+        ls ./
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File vcf = "${sample_id}.TNscope.vcf"
+        File vcf_index = "${sample_id}.TNscope.vcf.idx"
+
+    }
+}