init

.dockstore.yml

@@ -359,3 +359,12 @@ workflows:
     filters: # All tags, no branches
       branches:
         - vep-sv
+  - name: svannotate
+    subclass: WDL
+    publish: True
+    primaryDescriptorPath: /WGS_pipeline/svannotate.wdl
+    testParameterFiles:
+      - /test.json
+    filters: # All tags, no branches
+      branches:
+        - gatk-svannotate

WGS_pipeline/svannotate.wdl

@@ -0,0 +1,70 @@
+version 1.0
+# partially stolen from https://github.com/broadinstitute/long-read-pipelines/blob/ym_testing/wdl/SVAnnotate.wdl
+
+workflow SVAnnotate_workflow {
+    input {
+        String sample_id
+        File vcf
+        File coding_gtf
+        File noncoding_bed
+    }
+
+    call SVAnnotate {
+        input:
+            sample_id=sample_id,
+            vcf=vcf, 
+            coding_gtf=coding_gtf, 
+            noncoding_bed=noncoding_bed
+    }
+
+    output {
+        File vcf_anno = Standardize.vcf_anno
+        File vcf_anno_tbi = Standardize.vcf_anno_tbi
+    }
+}
+
+task SVAnnotate {
+    input {
+        File vcf
+        File coding_gtf
+        File noncoding_bed
+    }
+
+    Int disk_size = 5 + 5*ceil(size(vcf, "GB"))
+
+    command <<<
+        set -euxo pipefail
+
+        tabix ~{vcf}
+
+        gatk SVAnnotate -V ~{vcf} --non-coding-bed ~{noncoding_bed} --protein-coding-gtf ~{coding_gtf} -O ~{sample_id}.anno.vcf
+        bcftools view -Oz ~{sample_id}.anno.vcf > ~{sample_id}.anno.vcf.gz
+        tabix ~{sample_id}.anno.vcf.gz
+    >>>
+
+    output {
+        File vcf_anno = "~{sample_id}.anno.vcf.gz"
+        File vcf_anno_tbi = "~{sample_id}.anno.vcf.gz.tbi"
+    }
+
+    #########################
+    RuntimeAttr default_attr = object {
+        cpu_cores:          2,
+        mem_gb:             2,
+        disk_gb:            disk_size,
+        boot_disk_gb:       10,
+        preemptible_tries:  0,
+        max_retries:        0,
+        docker:             "quay.io/ymostovoy/lr-svannotate:latest"
+    }
+    RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
+    runtime {
+        cpu:                    select_first([runtime_attr.cpu_cores,         default_attr.cpu_cores])
+        memory:                 select_first([runtime_attr.mem_gb,            default_attr.mem_gb]) + " GiB"
+        disks: "local-disk " +  select_first([runtime_attr.disk_gb,           default_attr.disk_gb]) + " HDD"
+        bootDiskSizeGb:         select_first([runtime_attr.boot_disk_gb,      default_attr.boot_disk_gb])
+        preemptible:            select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
+        maxRetries:             select_first([runtime_attr.max_retries,       default_attr.max_retries])
+        docker:                 select_first([runtime_attr.docker,            default_attr.docker])
+    }
+}