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fixup: avoid awk column number selection
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j23414 committed Apr 5, 2024
1 parent 5930fcf commit 775ca33
Showing 1 changed file with 1 addition and 2 deletions.
3 changes: 1 addition & 2 deletions ingest/rules/nextclade.smk
Original file line number Diff line number Diff line change
Expand Up @@ -143,11 +143,10 @@ rule append_gene_coverage_columns:
"""
cp {input.metadata} {output.metadata_all}
for FILE in {input.gene_coverage}; do
export append_col=`awk 'NR==1 {{print $2}}' $FILE`
tsv-join -H \
--filter-file $FILE \
--key-fields {params.id_field} \
--append-fields $append_col \
--append-fields '*_coverage' \
--write-all ? \
{output.metadata_all} \
> results/temp_aggregate_gene_coverage.tsv
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