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fixup! Use "accession" column as ID column directly
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j23414 committed Aug 19, 2023
1 parent ac34243 commit 9dbccc4
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12 changes: 0 additions & 12 deletions Snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -83,18 +83,6 @@ rule decompress:
zstd -d -c {input.metadata} > {output.metadata}
"""

# rule wrangle_metadata:
# input:
# metadata="data/metadata_{serotype}.tsv",
# output:
# metadata="results/wrangled_metadata_{serotype}.tsv",
# params:
# strain_id=config.get("strain_id_field", "strain"), #accession
# shell:
# """
# csvtk -t rename -f strain -n strain_original {input.metadata} \
# | csvtk -t mutate -f {params.strain_id} -n strain > {output.metadata}
# """

rule filter:
"""
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