From 2d49dcbba63ffa6c2c74908e1a16c1be74393a97 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 16 Apr 2024 11:07:37 -0700 Subject: [PATCH] phylogenetic: Use inline root sequence MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Based on feedback from @jameshadfield in https://github.com/nextstrain/zika/pull/56#issuecomment-2058060422 Looking at the existing dataset files on S3, the 8 KiB root-sequence.json is pretty negligible when the main Auspice JSON is only 163 KiB. Nextstrain datasets are limited by the 500MB memory cap in Chrome,¹ so we'd be fine adding the root sequence inline. ¹ https://github.com/nextstrain/auspice/issues/1622 --- phylogenetic/rules/export.smk | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/phylogenetic/rules/export.smk b/phylogenetic/rules/export.smk index dcd1893..ac12351 100644 --- a/phylogenetic/rules/export.smk +++ b/phylogenetic/rules/export.smk @@ -17,8 +17,7 @@ rule export: auspice_config = lambda wildcard: "defaults/auspice_config.json" if wildcard.gene in ["genome"] else "defaults/auspice_config_N450.json" output: - auspice_json = "auspice/measles_{gene}.json", - root_sequence = "auspice/measles_{gene}_root-sequence.json" + auspice_json = "auspice/measles_{gene}.json" params: strain_id = config["strain_id_field"] shell: @@ -30,7 +29,6 @@ rule export: --node-data {input.branch_lengths} {input.nt_muts} {input.aa_muts} \ --colors {input.colors} \ --auspice-config {input.auspice_config} \ - --include-root-sequence \ + --include-root-sequence-inline \ --output {output.auspice_json} """ - \ No newline at end of file