From 0b47f81feec636f13bb8d0c39b16239ceeea5684 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Thu, 13 Nov 2025 11:15:40 -0800 Subject: [PATCH] ingest/extract_open_data: Do not compress intermediate files MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Use uncompressed outputs so that the uploaded files are no longer double compressed.¹ Once `upload-to-s3` supports compressed local files, we can go back to using compressed intermediate files. ¹ --- ingest/Snakefile | 4 ++-- ingest/build-configs/nextstrain-automation/config.yaml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ingest/Snakefile b/ingest/Snakefile index 965f0d43..ac5e56fb 100644 --- a/ingest/Snakefile +++ b/ingest/Snakefile @@ -48,8 +48,8 @@ rule extract_open_data: metadata="results/metadata.tsv", sequences="results/sequences.fasta", output: - metadata="results/metadata_open.tsv.zst", - sequences="results/sequences_open.fasta.zst", + metadata="results/metadata_open.tsv", + sequences="results/sequences_open.fasta", shell: """ augur filter --metadata {input.metadata} \ diff --git a/ingest/build-configs/nextstrain-automation/config.yaml b/ingest/build-configs/nextstrain-automation/config.yaml index e5e483b2..b9f9b9a2 100644 --- a/ingest/build-configs/nextstrain-automation/config.yaml +++ b/ingest/build-configs/nextstrain-automation/config.yaml @@ -22,8 +22,8 @@ upload: alignment_with_restricted.fasta.zst: results/alignment.fasta translations_with_restricted.zip: results/translations.zip - metadata.tsv.zst: results/metadata_open.tsv.zst - sequences.fasta.zst: results/sequences_open.fasta.zst + metadata.tsv.zst: results/metadata_open.tsv + sequences.fasta.zst: results/sequences_open.fasta cloudfront_domain: 'data.nextstrain.org'