From 28208dc50911882e534a1d57641c9f5c1f536194 Mon Sep 17 00:00:00 2001 From: Jonn Smith Date: Wed, 18 Dec 2024 16:28:37 -0500 Subject: [PATCH] Fixed typo in zarr output file. --- .../VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl b/wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl index d4b62676f..5ac5abaef 100644 --- a/wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl +++ b/wdl/pipelines/TechAgnostic/VariantCalling/SRJointCallGVCFsWithGenomicsDB.wdl @@ -527,17 +527,23 @@ workflow SRJointCallGVCFsWithGenomicsDB { Array[String] final_snpEff_genes = if defined(gcs_out_root_dir) then [select_first([FinalizeSnpEffGenes.gcs_dir])] else select_all(FunctionallyAnnotate.snpEff_genes) } + # Resolve the final joint Zarr file if we have created one: + if (do_zarr_conversion) { + File final_joint_zarr = select_first([FinalizeZarr.gcs_path, ConvertToZarr.zarr]) + } + output { File joint_vcf_out = select_first([FinalizeVETSVCF.gcs_path, GatherRescoredVcfs.output_vcf]) File joint_vcf_out_tbi = select_first([FinalizeVETSTBI.gcs_path, GatherRescoredVcfs.output_vcf_index]) File joint_mt = select_first([FinalizeHailMatrixTable.gcs_path, CreateHailMatrixTable.mt_tar]) - File joint_zarr = select_first([FinalizeZarr.gcs_path, ConvertToZarr.zarr]) Array[String] genomicsDB = select_first([final_genomicsdb_location, ImportGVCFsIntoGenomicsDB.output_genomicsdb]) + File? joint_zarr = final_joint_zarr Array[String]? snpEff_summary = final_snpeff_summary Array[String]? snpEff_genes = final_snpEff_genes + } }