From 1fd0a483ac1f61d8cd863addf268e1b1a91ec609 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 8 Sep 2023 16:38:07 -0400 Subject: [PATCH] small tweak to speed input processing and reduce temp file sizes --- pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl b/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl index 9d8410ecc..e6f822985 100644 --- a/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl +++ b/pipes/WDL/workflows/sarscov2_nextstrain_aligned_input.wdl @@ -13,7 +13,7 @@ workflow sarscov2_nextstrain_aligned_input { } input { - Array[File]+ aligned_sequences_fasta=["gs://nextstrain-data/files/ncov/open/aligned.fasta.xz"] + Array[File]+ aligned_sequences_fasta=["gs://nextstrain-data/files/ncov/open/aligned.fasta.zst"] Array[File]+ sample_metadata_tsvs=["gs://nextstrain-data/files/ncov/open/metadata.tsv.gz"] String build_name @@ -57,7 +57,7 @@ workflow sarscov2_nextstrain_aligned_input { call utils.zcat { input: infiles = aligned_sequences_fasta, - output_name = "all_samples_combined_assembly.fasta" + output_name = "all_samples_combined_assembly.fasta.xz" } #### merge metadata, compute derived cols