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Move accession to the first column of metadata_all.tsv
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During the merge of Usvi data and GenBank data, the accession field ended
up as the last column. This caused confusion as the first column was named
"genbank_accession" which could be mistaken for the strain ID.

This commit moves the "accession" column to the first column such that
"accession" and "genbank_accession" are next to each other; hopefully,
providing clarity that "accession" is being used as the strain ID, while
"genbank_accession" can be used to generate a url to the NCBI GenBank record
if provided.
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j23414 committed Feb 23, 2024
1 parent c710ca1 commit b68a6aa
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1 change: 1 addition & 0 deletions phylogenetic/rules/merge_sequences_usvi.smk
Original file line number Diff line number Diff line change
Expand Up @@ -43,5 +43,6 @@ rule append_usvi:
-n accession \
-e '$genbank_accession' \
| csvtk concat -tl - {input.usvi_metadata} \
| tsv-select -H -f accession --rest last \
> {output.metadata}
"""

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