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Ingest: remove reverse column from metadata TSV #209

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

Ingest: remove reverse column from metadata TSV #209

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

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@joverlee521
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joverlee521 commented Oct 13, 2023 •
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(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 joverlee521 mentioned this issue Oct 13, 2023
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joverlee521 added a commit that referenced this issue Oct 13, 2023
@joverlee521
Remove reverse column, associated script, and references
172561f 
The `reverse` column has effectively been replaced by `is_reverse_complement`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.
@joverlee521 joverlee521 linked a pull request Oct 13, 2023 that will close this issue
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@chaoran-chen
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Hi @joverlee521, thank you very much for pinging me! I don't use the reverse column.

@joverlee521 joverlee521 mentioned this issue Oct 16, 2023
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Remove reverse column, associated script, and references nextstrain/mpox
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@chaoran-chen @joverlee521