Open joverlee521 opened 1 month ago
Prompted by https://github.com/nextstrain/pathogen-repo-guide/pull/54#issuecomment-2229193810
Taking a closer look at the use of csvtk in the nextclade.smk
csvtk
https://github.com/nextstrain/pathogen-repo-guide/blob/06e6f275daca928ba0d39f49b621a8aadfc0cff2/ingest/rules/nextclade.smk#L78-L85
Seems like we can replace the two csvtk commands in the pipeline with tsv-select and augur curate rename so that we are not blocked by https://github.com/shenwei356/csvtk/issues/283.
tsv-select
augur curate rename
Replacing csvtk rename2 with augur curate rename will take a little extra munging by either:
csvtk rename2
Prompted by https://github.com/nextstrain/pathogen-repo-guide/pull/54#issuecomment-2229193810
Taking a closer look at the use of
csvtk
in the nextclade.smkhttps://github.com/nextstrain/pathogen-repo-guide/blob/06e6f275daca928ba0d39f49b621a8aadfc0cff2/ingest/rules/nextclade.smk#L78-L85
Seems like we can replace the two
csvtk
commands in the pipeline withtsv-select
andaugur curate rename
so that we are not blocked by https://github.com/shenwei356/csvtk/issues/283.