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Update top-level name #12

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merged 3 commits into from
Apr 19, 2024
Merged

Update top-level name #12

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a9ce080
Reference new top-level name in CI build target
victorlin Apr 19, 2024
f8df5ff
Reference new top-level name in AWS Batch script
victorlin Apr 19, 2024
cb887f6
Reference new top-level name in quickstart build
victorlin Apr 19, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,4 +8,4 @@ jobs:
ci:
uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
with:
build-args: auspice/flu_avian_h5n1_ha.json
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build-args: auspice/avian-flu_h5n1_ha.json
4 changes: 2 additions & 2 deletions batch.py
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Expand Up @@ -30,8 +30,8 @@
for segment in params.segments:
call = ['nextstrain', 'build', '--aws-batch', '.', '-j 1']
targets = []
targets.append('auspice/flu_avian_%s_%s_tree.json'%(subtype, segment))
targets.append('auspice/flu_avian_%s_%s_meta.json'%(subtype, segment))
targets.append('auspice/avian-flu_%s_%s_tree.json'%(subtype, segment))
targets.append('auspice/avian-flu_%s_%s_meta.json'%(subtype, segment))
call.extend(targets)
print(' '.join(call))
log = open('logs/%s_%s.txt'%(subtype, segment), 'w')
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4 changes: 2 additions & 2 deletions quickstart-build/Snakefile
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Expand Up @@ -15,7 +15,7 @@ SEGMENTS = ["ha"]
generated JSON files in the auspice folder for each subtype and segment."""
rule all:
input:
auspice_json = expand("auspice/flu_avian_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)
auspice_json = expand("auspice/avian-flu_{subtype}_{segment}.json", subtype=SUBTYPES, segment=SEGMENTS)

"""Specify all input files here. For this build, you'll start with input sequences
from the example_data folder, which contain metadata information in the
Expand Down Expand Up @@ -305,7 +305,7 @@ rule export:
node_data = node_data_by_wildcards,
auspice_config = files.auspice_config
output:
auspice_json = "auspice/flu_avian_{subtype}_{segment}.json"
auspice_json = "auspice/avian-flu_{subtype}_{segment}.json"
shell:
"""
augur export v2 \
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