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Remove ndjson scripts from existing pathogen repos #28

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9 of 16 tasks
victorlin opened this issue Oct 17, 2023 · 1 comment
Open
9 of 16 tasks

Remove ndjson scripts from existing pathogen repos #28

victorlin opened this issue Oct 17, 2023 · 1 comment
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@victorlin

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@victorlin
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victorlin commented Oct 17, 2023 •
edited by joverlee521
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Follow-up to #1. Copying some useful text from the Google doc linked there:

csv-to-ndjson / tsv-to-ndjson

No longer needed as this can be done with augur curate passthru.

We can remove this script from the following repos (found with code search) as we update their workflows to use augur curate. 

fasta-to-ndjson

No longer needed as this can be done with a combination of augur parse and augur curate passthru. 

We can remove this script from the following repos (found with code search) as we update their workflows.

  • monkeypox
  • Rsv
  • Dengue
  • Zika
  • Ebola (won't show up in code search as it's on a branch)

ndjson-to-tsv-and-fasta

No longer needed as this can be done with augur curate passthru. 

We can remove this script from the following repos (found with code search) as we update their workflows.
@victorlin victorlin self-assigned this Oct 17, 2023
@victorlin victorlin mentioned this issue Oct 26, 2023
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jameshadfield added a commit to nextstrain/hbv that referenced this issue Mar 5, 2024
@jameshadfield
Remove ndjson scripts
ec796da 
Brings the ingest repo in-line with the general
pattern of other pathogen ingests. See
<#9>
for more context.

Note that we no longer vendor ndjson scripts as
their functionality is now available via `augur
curate passthru` (sic); see
<nextstrain/ingest#28>
for more.

Closes <#9>
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I consider this slightly blocked by a bug in augur curate passthru.

@victorlin victorlin added the blocked Dependent on external development label Jun 25, 2024
@joverlee521 joverlee521 removed the blocked Dependent on external development label Jul 15, 2024
@joverlee521 joverlee521 mentioned this issue Jul 15, 2024
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