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Rename metadata column from isolate_id to gisaid_epi_isl #179

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merged 2 commits into from
Oct 10, 2024
Merged

Rename metadata column from isolate_id to gisaid_epi_isl #179

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ce3030d
Fix whitespace
joverlee521 Sep 10, 2024
2e8211d
Rename metadata column from `isolate_id` to `gisaid_epi_isl`
joverlee521 Sep 10, 2024
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3 changes: 1 addition & 2 deletions nextclade/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -415,7 +415,7 @@ rule export:
date=datetime.datetime.utcnow().strftime("%Y-%m-%d"),
shell:
"""
tsv-select -H -f {params.select_fields} {input.metadata} > {input.metadata}.tmp
tsv-select -H -f {params.select_fields} {input.metadata} > {input.metadata}.tmp
augur export v2 \
--tree {input.tree} \
--metadata {input.metadata}.tmp \
Expand Down Expand Up @@ -494,4 +494,3 @@ rule clean_all:
rm -rf datasets
rm -rf data/
"""

2 changes: 1 addition & 1 deletion profiles/upload.yaml
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Expand Up @@ -25,7 +25,7 @@ fasta_fields:
- strain
- virus
- segment
- isolate_id
- gisaid_epi_isl
- accession
- date
- date_submitted
Expand Down