From 610b1c538a2bca5a7893c406c9f628b979dfbfca Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Thu, 21 Nov 2024 10:58:43 -0500 Subject: [PATCH 1/2] switch back to gsutil cp --- scripts/variantstore/wdl/GvsExtractCallset.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index a62bccb4cd5..b19ec5211bf 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -573,7 +573,7 @@ task CreateManifestAndOptionallyCopyOutputs { if [ -n "$OUTPUT_GCS_DIR" ]; then # 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} + cat vcf_manifest.txt | gsutil cp - ${OUTPUT_GCS_DIR} fi >>> output { From c5f5f0bb5410811cb45d4e9b95c5fd433d66729b Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Thu, 21 Nov 2024 12:46:41 -0500 Subject: [PATCH 2/2] use xargs instead --- scripts/variantstore/wdl/GvsExtractCallset.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index b19ec5211bf..97d0033f9be 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -573,7 +573,7 @@ task CreateManifestAndOptionallyCopyOutputs { if [ -n "$OUTPUT_GCS_DIR" ]; then # Copy VCFs, indexes and the manifest to the output directory. echo manifest.txt >> vcf_manifest.txt - cat vcf_manifest.txt | gsutil cp - ${OUTPUT_GCS_DIR} + cat vcf_manifest.txt | xargs -IFILE gsutil cp FILE ${OUTPUT_GCS_DIR} fi >>> output {