vdb/download: Add --prioritized_seqs_file option
#176
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Allow users to define prioritized sequence accessions for a strain when the duplicate resolve method is `split_passage`. This flag could be extended for other resolve methods, but we are not actively using them in seasonal flu workflows so punting for now. The file is expected to be a TSV file with a `strain` and `accession` column where the `strain` column only contains unique strain names. With the seasonal flu's pattern of downloading each segment separately,¹ the file should contain sequence accessions for a single segment. ¹ <https://github.com/nextstrain/seasonal-flu/blob/73b8294906da99a6abd26f543edd68dfd6e63d0e/workflow/snakemake_rules/download_from_fauna.smk#L69>
genehack
approved these changes
Jan 14, 2025
3 tasks
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Description of proposed changes
Allow users to define prioritized sequence accessions for a strain when the duplicate resolve method is
split_passage. This flag could be extended for other resolve methods, but we are not actively using them in seasonal flu workflows so punting for now.The file is expected to be a TSV file with a
strainandaccessioncolumn where thestraincolumn only contains unique strain names. With the seasonal flu's pattern of downloading each segment separately,¹ the file should contain sequence accessions for a single segment.¹ https://github.com/nextstrain/seasonal-flu/blob/73b8294906da99a6abd26f543edd68dfd6e63d0e/workflow/snakemake_rules/download_from_fauna.smk#L69
Related issue(s)
Part of #174
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