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Use GatherVcfsCloud in GvsCreateFilterSet.wdl #7241

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merged 8 commits into from
May 6, 2021
Merged

Use GatherVcfsCloud in GvsCreateFilterSet.wdl #7241

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3b960b1
gathervcfscloud, add branch to dockstore
mmorgantaylor May 5, 2021
52fe09a
fix gatk call and tabix call
mmorgantaylor May 5, 2021
009b854
fix jar, and tabix path
mmorgantaylor May 5, 2021
dabdb6e
fix input flag
mmorgantaylor May 5, 2021
492fc1d
try different docker/jar
mmorgantaylor May 5, 2021
8320490
tabix works properly in this docker
mmorgantaylor May 5, 2021
ad653bd
clean up
mmorgantaylor May 5, 2021
919f47b
remove feature branch from dockstore
mmorgantaylor May 6, 2021
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31 changes: 23 additions & 8 deletions scripts/variantstore/wdl/GvsCreateFilterSet.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,8 @@ workflow GvsCreateFilterSet {
input_vcfs = ExtractFilterTask.output_vcf,
input_vcfs_indexes = ExtractFilterTask.output_vcf_index,
output_vcf_name = "${output_file_base_name}.vcf.gz",
preemptible_tries = 3
preemptible_tries = 3,
gatk_override = gatk_override
}

call IndelsVariantRecalibrator {
Expand Down Expand Up @@ -465,21 +466,35 @@ task UploadFilterSetToBQ {
Array[File] input_vcfs
Array[File] input_vcfs_indexes
String output_vcf_name

File? gatk_override
Int preemptible_tries
}

Int disk_size = ceil(size(input_vcfs, "GiB") * 2.5) + 10

# Using MergeVcfs instead of GatherVcfs so we can create indices
# See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
parameter_meta {
input_vcfs: {
localization_optional: true
}
input_vcfs_indexes: {
localization_optional: true
}
}

command {
java -Xms2000m -jar /usr/gitc/picard.jar \
MergeVcfs \
INPUT=~{sep=' INPUT=' input_vcfs} \
OUTPUT=~{output_vcf_name}
export GATK_LOCAL_JAR=~{default="/root/gatk.jar" gatk_override}

gatk --java-options -Xms3g GatherVcfsCloud \
--ignore-safety-checks --gather-type BLOCK \
-I ~{sep=' -I ' input_vcfs} \
--output ~{output_vcf_name}

tabix ~{output_vcf_name}

}
runtime {
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856"
docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_d8a72b825eab2d979c8877448c0ca948fd9b34c7_change_to_hwe"
preemptible: preemptible_tries
memory: "3 GiB"
disks: "local-disk ~{disk_size} HDD"
Expand Down