Ingest: remove reverse column from metadata TSV
#209
Comments
2 tasks
joverlee521
added a commit
that referenced
this issue
Oct 13, 2023
The `reverse` column has effectively been replaced by `is_reverse_complement` from the Nextclade output. The script `ingest/bin/reverse_reversed_sequences.py` is no longer used because it's function is now built into Nextclade. Resolves #209.
1 task
|
Hi @joverlee521, thank you very much for pinging me! I don't use the |
joverlee521
added a commit
that referenced
this issue
Jul 15, 2024
Previously this was filled in with empty strings by the custom `ndjson-to-tsv-and-fasta` script. We've replaced vendored scripts with `augur curate` commands, so we no longer need this script, but now the workflow errors on this unexpected column. As discussed in #209, this column is not used anyways so just remove it.
joverlee521
added a commit
that referenced
this issue
Jul 15, 2024
Previously this was filled in with empty strings by the custom `ndjson-to-tsv-and-fasta` script. We've replaced vendored scripts with `augur curate` commands, so we no longer need this script, but now the workflow errors on this unexpected column. As discussed in #209, this column is not used anyways so just remove it.
2 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
(Originally flagged the obsolete
reversecolumn in #207 (comment))Reverse complement sequences were initially manually flagged by the
reversecolumn added in #79.Since Nextclade v2.2.0, there's a built-in
--retry-reverse-complementoption that adds a new columnisReverseComplement. This feature was used in the ingest pipeline starting from #89. Then in #94, theingest/bin/reverse_reversed_sequences.pyscript was replaced with the built-in Nextclade functionality as well.In #191, the phylogenetic pipeline switched over from using the
reversecolumn to theis_reverse_complementcolumn output from Nextclade. This seemingly makes thereversecolumn obsolete. When checking the latest metadata TSV (2023-10-13), thereversecolumn is completely empty.From my point of view, we can just remove the
reversecolumn from the metadata.tsv file, but wanted to confirm with other users of the pipeline/metadata.tsv file (cc: @corneliusroemer, @chaoran-chen).The text was updated successfully, but these errors were encountered: