添加 'tasks/manta.wdl'

tasks/manta.wdl

@@ -0,0 +1,47 @@
+task manta_calling{
+    File tumor_bam
+    File tumor_bam_bai
+    File normal_bam
+    File normal_bam_bai
+    String ref_fasta
+    File ref_dir
+    String sample_id
+    
+    String docker
+    String cluster_config
+    String disk_size
+
+    
+    String out_dir = "${sample_id}_result"
+    command <<<
+    set -exo pipefail
+    nt=$(nproc)
+    /home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \
+    --normalBam ${normal_bam} \
+    --tumorBam ${tumor_bam} \
+    --referenceFasta ${ref_dir}/${ref_fasta} \
+    --runDir ${out_dir}
+    
+    ls ${out_dir}
+
+    python2.7 ${out_dir}/runWorkflow.py -m local -j $nt
+
+    ls ${out_dir}
+
+    tar cvf ${out_dir}.tar ${out_dir}
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+
+    }
+
+    output{
+        File out_file = "${out_dir}.tar"
+        File manta_indel_vcf = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz"
+        File manta_indel_vcf_index = "${out_dir}/results/variants/candidateSmallIndels.vcf.gz.tbi"
+    }
+}