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VS-1526 - Fix error in Extract Manifest Creation causing it to run forever. #9034

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merged 6 commits into from
Nov 13, 2024
Merged

VS-1526 - Fix error in Extract Manifest Creation causing it to run forever. #9034

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f96e258
Fixed an error in localization_optional
gbggrant Nov 5, 2024
f15b649
Fix for gcloud
gbggrant Nov 5, 2024
17476db
I should learn how to type. It would be a valuable skill!
gbggrant Nov 5, 2024
2615da8
Small improvement.
gbggrant Nov 5, 2024
9f4d215
Clean ups
gbggrant Nov 5, 2024
3e02be5
Merge remote-tracking branch 'origin/ah_var_store' into gg_VS-1526_Do…
gbggrant Nov 13, 2024
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1 change: 1 addition & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -173,6 +173,7 @@ workflows:
branches:
- master
- ah_var_store
- gg_VS-1526_DontRunForever
tags:
- /.*/
- name: GvsImportGenomes
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13 changes: 9 additions & 4 deletions scripts/variantstore/wdl/GvsExtractCallset.wdl
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Expand Up @@ -516,7 +516,7 @@ task CreateManifestAndOptionallyCopyOutputs {
String? output_gcs_dir
String cloud_sdk_docker
}
meta {
parameter_meta {
# Not `volatile: true` since there shouldn't be a need to re-run this if there has already been a successful execution.
output_vcfs: {
localization_optional: true
Expand All @@ -540,6 +540,9 @@ task CreateManifestAndOptionallyCopyOutputs {
declare -a output_vcf_bytes=(~{sep=' ' output_vcf_bytes})
declare -a output_vcf_index_bytes=(~{sep=' ' output_vcf_index_bytes})

# (Possibly) create a manifest of VCFs and indexes to bulk copy with `gcloud storage cp`.
echo -n > vcf_manifest.txt
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echo -n >> manifest_lines.txt
for (( i=0; i<${#interval_indices[@]}; ++i));
do
Expand All @@ -551,8 +554,8 @@ task CreateManifestAndOptionallyCopyOutputs {
LOCAL_VCF_INDEX=$(basename $OUTPUT_VCF_INDEX)

if [ -n "${OUTPUT_GCS_DIR}" ]; then
gsutil cp $OUTPUT_VCF ${OUTPUT_GCS_DIR}/
gsutil cp $OUTPUT_VCF_INDEX ${OUTPUT_GCS_DIR}/
echo $OUTPUT_VCF >> vcf_manifest.txt
echo $OUTPUT_VCF_INDEX >> vcf_manifest.txt
OUTPUT_FILE_DEST="${OUTPUT_GCS_DIR}/$LOCAL_VCF"
OUTPUT_FILE_INDEX_DEST="${OUTPUT_GCS_DIR}/$LOCAL_VCF_INDEX"
else
Expand All @@ -568,7 +571,9 @@ task CreateManifestAndOptionallyCopyOutputs {
sort -n manifest_lines.txt | cut -d',' -f 2- >> manifest.txt

if [ -n "$OUTPUT_GCS_DIR" ]; then
gsutil cp manifest.txt ${OUTPUT_GCS_DIR}/
# Copy VCFs, indexes and the manifest to the output directory.
echo manifest.txt >> vcf_manifest.txt
cat vcf_manifest.txt | gcloud storage cp -I ${OUTPUT_GCS_DIR}
fi
>>>
output {
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