From b88bc946c4185cccaf6faedc242bcedd98c23bdd Mon Sep 17 00:00:00 2001
From: Shadi Zaheri <szaheri@broadinstitute.org>
Date: Sun, 11 Aug 2024 13:35:11 -0400
Subject: [PATCH] to split vcf

---
 wdl/tasks/Utility/split_vcf.wdl | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 wdl/tasks/Utility/split_vcf.wdl

diff --git a/wdl/tasks/Utility/split_vcf.wdl b/wdl/tasks/Utility/split_vcf.wdl
new file mode 100644
index 000000000..3d5057067
--- /dev/null
+++ b/wdl/tasks/Utility/split_vcf.wdl
@@ -0,0 +1,60 @@
+version 1.0
+
+workflow SplitVCFWorkflow {
+    input {
+        File joint_vcf
+        Array[String] regions
+        Array[String] sample_names
+    }
+
+    scatter (region in regions) {
+        scatter (samplename in sample_names) {
+            call SplitVCFbySample {
+                input:
+                    joint_vcf = joint_vcf,
+                    region = region,
+                    sample_name = samplename
+            }
+        }
+    }
+
+    output {
+        Array[File] single_sample_vcfs = flatten(SplitVCFbySample.single_sample_vcf)
+        Array[File] single_sample_vcf_tbis = flatten(SplitVCFbySample.single_sample_vcf_tbi)
+    }
+}
+
+task SplitVCFbySample {
+    input {
+        File joint_vcf
+        String region
+        String sample_name
+    }
+
+    command <<<
+        set -euxo pipefail
+
+        bcftools index ${joint_vcf}
+
+        bcftools view -s ${sample_name} ${joint_vcf} -r ${region} -o ${sample_name}.subset.g.vcf.gz
+
+        tabix -p vcf ${sample_name}.subset.g.vcf.gz
+    >>>
+
+    output {
+        File single_sample_vcf = "${sample_name}.subset.g.vcf.gz"
+        File single_sample_vcf_tbi = "${sample_name}.subset.g.vcf.gz.tbi"
+    }
+
+    runtime {
+        cpu: 1
+        memory: "64 GiB"
+        disks: "local-disk ${disk_size} HDD"
+        bootDiskSizeGb: 10
+        preemptible: 0
+        maxRetries: 1
+        docker: "us.gcr.io/broad-dsp-lrma/lr-basic:0.1.1"
+    }
+
+    Int disk_size = ceil(2 * size(joint_vcf, "GiB")) + 1
+}