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Document the notable columns in merging USVI and GenBank data
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In cases like this where a column name is ambiguous ('accession' and 'genbank_accession'),
bring this context out of commit messages/PRs and into the code itself.
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j23414 committed Feb 23, 2024
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8 changes: 7 additions & 1 deletion phylogenetic/rules/merge_sequences_usvi.smk
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Expand Up @@ -22,7 +22,13 @@ This part of the workflow usually includes the following steps:
"""

rule append_usvi:
"""Appending USVI sequences"""
"""Appending USVI sequences
Notable columns:
- accession: Either the GenBank accession or USVI accession.
- genbank_accession: GenBank accession for Auspice to generate a URL to the NCBI GenBank record. Empty for USVI sequences.
- url: URL used in Auspice, to either link to the USVI github repo (https://github.com/blab/zika-usvi/) or link to the NCBI GenBank record ('https://www.ncbi.nlm.nih.gov/nuccore/*')
"""
input:
sequences = "data/sequences.fasta",
metadata = "data/metadata.tsv",
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