上传文件至 'tasks'

tasks/BQSR.wdl

@@ -0,0 +1,76 @@
+task Sentieon_BQSR{
+    File ref_dir
+    File dbsnp_dir
+    File dbmills_dir
+
+    String sample_id
+    String ref_fasta
+    String dbsnp
+    String db_mills
+
+    File deduped_bam
+    File deduped_bam_index
+
+    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)
+
+        if [${regions}];then
+            INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
+        else
+            INTERVAL=""
+        fi
+
+        sentieon driver -t $nt \
+        -r ${ref_dir}/${ref_fasta} -i ${deduped_bam} \
+        $INTERVAL \
+        --algo QualCal \
+        -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+        ${sample_id}_recal_data.table
+
+        sentieon driver -t $nt \
+        -r ${ref_dir}/${ref_fasta} -i ${deduped_bam} \
+        -q ${sample_id}_recal_data.table \
+        --algo QualCal \
+        -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
+        ${sample_id}_recal_data.table.post \
+        --algo ReadWriter ${sample_id}.sorted.deduped.recaled.bam
+
+        sentieon driver -t $nt --algo QualCal \
+        --plot --before ${sample_id}_recal_data.table --after ${sample_id}_recal_data.table.post ${sample_id}_recal_data.csv
+
+        sentieon plot bqsr -o ${sample_id}_bqsrreport.pdf ${sample_id}_recal_data.csv
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+
+    }
+
+    output{
+        File recal_table = "${sample_id}_recal_data.table"
+        File recal_post = "${sample_id}_recal_data.table.post"
+        File recaled_bam = "${sample_id}.sorted.deduped.recaled.bam"
+        File recaled_bam_index = "${sample_id}.sorted.deduped.recaled.bam.bai"
+        File recal_csv = "${sample_id}_recal_data.csv"
+        File bqsrreport_pdf = "${sample_id}_bqsrreport.pdf"
+
+    }
+}