Ingest nextclade updates #54
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
I guess I've never tested running this path of the ingest workflow.
Error showed up when I tried to run the workflow with the Nextclade
config.
```
nextstrain build ingest results/metadata.tsv --config ncbi_taxon_id='64320' --configfile defaults/nextclade_config.yaml --forceall -n
Config file defaults/config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
MissingInputException in rule join_metadata_and_nextclade in file /nextstrain/build/ingest/rules/nextclade.smk, line 64:
Missing input files for rule join_metadata_and_nextclade:
output: results/metadata.tsv
affected files:
config/nextclade_field_map.tsv
```
This was originally copied from mpox and `lineage` is a very mpox specific field that is not usually included in the Nextclade output TSV.
This was written before Nextclade v3 was officially released. Nextclade v3 been out for >6 months now and all new Nextclade datasets are expected to be v3.
|
I was running into a weird error when testing this PR with mpox: Turns out the root error is coming from I'm going to drop dc9ac25 for now and follow up in a separate change -> see |
joverlee521
force-pushed
the
ingest-nextclade-updates
branch
from
dc9ac25
to
b6f07a6
Compare
genehack
approved these changes
Jul 16, 2024
|
@joverlee521 Oh no, so fix-quotes, which is a workaround for csvtk's lack of TSV support has its own quirks? This strengthens my opinion that we should just never use csvtk for TSVs 🙃 I see that this is exactly what you're doing in #55 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
Various small fixes for the Nextclade rules of the ingest workflow.
See commits for details.
Related issue(s)
Resolves #47
Related to https://github.com/nextstrain/private/issues/97
Checklist