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feat: use nightly nextclade tree #1170

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feat: use nightly nextclade tree #1170

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c3cd0a3
feat: use nightly nextclade tree
ivan-aksamentov Jan 28, 2025
00ce581
fix: flag output directory with directory()
ivan-aksamentov Jan 28, 2025
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12 changes: 9 additions & 3 deletions workflow/snakemake_rules/main_workflow.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -455,14 +455,20 @@ rule prepare_nextclade:
Downloading reference files for nextclade (used for alignment and qc).
"""
output:
nextclade_dataset = "data/sars-cov-2-nextclade-defaults.zip",
nextclade_dataset = directory("data/sars-cov-2-nextclade-defaults"),
params:
name = config["nextclade_dataset"],
conda: config["conda_environment"]
shell:
r"""
nextclade --version
nextclade dataset get --name {params.name} --output-zip {output.nextclade_dataset}
nextclade dataset get --name {params.name} --output-dir {output.nextclade_dataset}

# override tree.json with nightly tree
curl -fsSL \
-o {output.nextclade_dataset}/tree.json \
-H "Accept: application/vnd.nextstrain.dataset.main+json;q=1, application/json;q=0.9, text/plain;q=0.8, */*;q=0.1" \
"https://nextstrain.org/staging/nextclade/sars-cov-2"
"""

rule build_align:
Expand All @@ -473,7 +479,7 @@ rule build_align:
"""
input:
sequences = rules.combine_samples.output.sequences,
nextclade_dataset = "data/sars-cov-2-nextclade-defaults.zip",
nextclade_dataset = "data/sars-cov-2-nextclade-defaults",
output:
alignment = "results/{build_name}/aligned.fasta",
nextclade_qc = 'results/{build_name}/nextclade_qc.tsv',
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