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Run Nextclade on all 8 genes for H1 and H3 #185

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merged 2 commits into from
Oct 23, 2024
Merged

Run Nextclade on all 8 genes for H1 and H3 #185

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3780fc0
Run Nextclade on all 8 genes for H1 and H3
huddlej Oct 15, 2024
582236f
Use full Nextclade names for all gene segments
huddlej Oct 15, 2024
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9 changes: 9 additions & 0 deletions profiles/nextclade.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,12 @@ s3_dst: "s3://nextstrain-data-private/files/workflows/seasonal-flu"
segments:
- ha
- na
- pb2
- pb1
- pa
- np
- mp
- ns

builds:
h1n1pdm:
Expand All @@ -15,3 +21,6 @@ builds:
lineage: h3n2
vic:
lineage: vic
segments:
- ha
- na
4 changes: 2 additions & 2 deletions profiles/nextclade/run-nextclade.smk
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Expand Up @@ -4,7 +4,7 @@ rule upload_all_nextclade_files:
"data/upload/s3/{filetype}_{lineage}_{segment}.done".format(filetype=filetype, lineage=build["lineage"], segment=segment)
for filetype in ("alignment", "nextclade")
for build in config["builds"].values()
for segment in config["segments"]
for segment in build.get("segments", config["segments"])
]

rule get_nextclade_dataset_for_lineage_and_segment:
Expand All @@ -13,7 +13,7 @@ rule get_nextclade_dataset_for_lineage_and_segment:
shell:
"""
nextclade3 dataset get \
-n flu_{wildcards.lineage}_{wildcards.segment} \
-n 'nextstrain/flu/{wildcards.lineage}/{wildcards.segment}' \
--output-dir {output.nextclade_dir}
"""

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