上传文件至 'tasks'

tasks/delly.wdl

@@ -0,0 +1,42 @@
+task delly{
+    String sample
+    File ref_dir
+    String fasta
+    File sample_tsv
+    File tumor_bam
+    File tumor_bam_index
+    File normal_bam
+    File normal_bam_index
+    String docker
+    String cluster_config
+    String disk_size
+
+    command<<<
+    /home/delly call -o ${sample}_delly.bcf \
+    -g ${ref_dir}/${fasta} \
+    ${tumor_bam} ${normal_bam}
+
+    /home/delly filter -p -f somatic \
+    -o ${sample}_delly.somatic.bcf -s ${sample_tsv} ${sample}_delly.bcf
+
+    bcftools convert -O v -o ${sample}_delly.somatic.vcf ${sample}_delly.somatic.bcf
+
+    vcftools --vcf ${sample}_delly.somatic.vcf \
+    --out ${sample}_delly.somatic.PASS \
+    --recode --recode-INFO-all --remove-filtered-all
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File somatic_bcf = "${sample}_delly.somatic.bcf"
+        File somatic_vcf = "${sample}_delly.somatic.vcf"
+        File pass_vcf = "${sample}_delly.somatic.PASS.recode.vcf"
+    }
+
+}