diff --git a/scripts/variantstore/wdl/GvsExtractCallset.wdl b/scripts/variantstore/wdl/GvsExtractCallset.wdl index 8e98c67a22e..87def334984 100644 --- a/scripts/variantstore/wdl/GvsExtractCallset.wdl +++ b/scripts/variantstore/wdl/GvsExtractCallset.wdl @@ -2,7 +2,7 @@ version 1.0 import "GvsUtils.wdl" as Utils -# A comment? +# A comment?? workflow GvsExtractCallset { input { @@ -533,12 +533,14 @@ task CreateManifestAndOptionallyCopyOutputs { echo -n >> manifest_lines.txt for (( i=0; i<${#interval_indices[@]}; ++i)); do - echo "Interval " + i + echo "Interval " + $i OUTPUT_VCF=${output_vcfs[$i]} - LOCAL_VCF=basename $OUTPUT_VCF + LOCAL_VCF=$(basename $OUTPUT_VCF) OUTPUT_VCF_INDEX=${output_vcf_indices[$i]} - LOCAL_VCF_INDEX=basename $OUTPUT_VCF_INDEX + LOCAL_VCF_INDEX=$(basename $OUTPUT_VCF_INDEX) + + echo ${interval_indices[$i]},${OUTPUT_FILE_DEST},${output_vcf_bytes[$i]},${OUTPUT_FILE_INDEX_DEST},${output_vcf_index_bytes[$i]} if [ -n "${OUTPUT_GCS_DIR}" ]; then gsutil cp $OUTPUT_VCF ${OUTPUT_GCS_DIR}/