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Snakefile_RSV
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Snakefile_RSV
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rule fetch_and_rename:
input:
"config/{lineage}_old_to_new.json"
output:
"auspice/{prefix}renamed_{lineage}.json"
params:
key = "renamed_clade"
shell:
"""
python3 scripts/rename_old_clades_RSV.py --lineage {wildcards.lineage} \
--clade-map {input} \
--key {params.key} \
--output {output}
"""
rule suggest_new_clades:
input:
renamed_auspice = "auspice/{prefix}renamed_{lineage}.json",
clade_map = "config/{lineage}_old_to_new.json",
weights = "config/weights.json",
output:
"auspice/{prefix}suggested_{lineage}.json"
params:
old_key = "renamed_clade",
new_key = "new_clade"
shell:
"""
python3 scripts/add_new_clades.py --input {input.renamed_auspice} \
--clade-map {input.clade_map} \
--weights {input.weights} \
--lineage {wildcards.lineage} \
--add-to-existing \
--old-key {params.old_key} --new-key {params.new_key} \
--output {output}
"""
rule add_provenance:
input:
"auspice/{prefix}suggested_{lineage}_{resolution}.json"
output:
"auspice/{prefix}with-provenance_{lineage}_{resolution}.json"
params:
key = "new_clade"
shell:
"""
python3 scripts/add_provenance.py --input {input} --key {params.key}\
--output {output}
"""