Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ingest: remove reverse column from metadata TSV #209

Closed
joverlee521 opened this issue Oct 13, 2023 · 1 comment · Fixed by #263 · May be fixed by #210
Closed

Ingest: remove reverse column from metadata TSV #209

joverlee521 opened this issue Oct 13, 2023 · 1 comment · Fixed by #263 · May be fixed by #210

Comments

@joverlee521
Copy link
Contributor

joverlee521 commented Oct 13, 2023

(Originally flagged the obsolete reverse column in #207 (comment))

Reverse complement sequences were initially manually flagged by the reverse column added in #79.

Since Nextclade v2.2.0, there's a built-in --retry-reverse-complement option that adds a new column isReverseComplement. This feature was used in the ingest pipeline starting from #89. Then in #94, the ingest/bin/reverse_reversed_sequences.py script was replaced with the built-in Nextclade functionality as well.

In #191, the phylogenetic pipeline switched over from using the reverse column to the is_reverse_complement column output from Nextclade. This seemingly makes the reverse column obsolete. When checking the latest metadata TSV (2023-10-13), the reverse column is completely empty.

From my point of view, we can just remove the reverse column from the metadata.tsv file, but wanted to confirm with other users of the pipeline/metadata.tsv file (cc: @corneliusroemer, @chaoran-chen).

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The `reverse` column has effectively been replaced by `is_reverse_complement`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.
@chaoran-chen
Copy link
Contributor

Hi @joverlee521, thank you very much for pinging me! I don't use the reverse column.

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.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
2 participants