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phylogenetic: Use inline root sequence
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Based on feedback from @jameshadfield in
nextstrain/zika#56 (comment)

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.

This ensures that our uploads will include the root sequence so that
they don't get out-of-sync with the main Auspice JSON.

¹ nextstrain/auspice#1622
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joverlee521 committed Apr 16, 2024
1 parent 9b93e70 commit a9b3033
Showing 1 changed file with 2 additions and 4 deletions.
6 changes: 2 additions & 4 deletions phylogenetic/rules/export.smk
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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}
"""

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