Assign genotypes using Nextclade dataset and visualize on tree #36
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ingest/rules/nextclade.smk
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| --name={params.dataset_name:q} \ | ||
| --output-zip={output.dataset} \ | ||
| --verbose \ | ||
| --server=https://data.master.clades.nextstrain.org/v3 |
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i wonder if it's worth parameterizing this too?
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After the nextclade dataset is officially released, the --server argument will be completely removed, and so I think it's better not to parameterize this, unless I'm misunderstanding your comment.
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Looks great to me. In testing, this just worked locally as well. |
| privateNucMutations.reversionSubstitutions private_reversionSubstitutions | ||
| privateNucMutations.labeledSubstitutions private_labeledSubstitutions | ||
| privateNucMutations.unlabeledSubstitutions private_unlabeledSubstitutions | ||
| privateNucMutations.totalReversionSubstitutions private_totalReversionSubstitutions | ||
| privateNucMutations.totalLabeledSubstitutions private_totalLabeledSubstitutions | ||
| privateNucMutations.totalUnlabeledSubstitutions private_totalUnlabeledSubstitutions | ||
| privateNucMutations.totalPrivateSubstitutions private_totalPrivateSubstitutions | ||
| qc.snpClusters.clusteredSNPs private_SNPclusters | ||
| qc.snpClusters.totalSNPs private_totalSNPclusters |
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Slight nitpick here to either use all camelCase or all snake_case for the column names.
| nextclade="results/nextclade.tsv", | ||
| alignment="results/alignment.fasta", | ||
| translations="results/translations.zip", |
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Since we are outputing these files, should they get uploaded to S3 in our automated workflow?
This should just involve adding them to the files_to_upload config parameter in ingest/build-configs/nextstrain-automation/config.yaml.
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For nextclade? Do we do this for other pathogens?
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Yup, we upload some combination of Nextclade output files in ncov-ingest and mpox/ingest.
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Ah of course! I was reading this as the nextclade dataset creation outputs but it's not!
Call genotypes using Nextclade dataset and add them to the metadata output of ingest. After the measles Nextclade dataset is officially released, we can remove `--server=https://data.master.clades.nextstrain.org/v3` from the `get_nextclade_dataset` rule.
1. Add Nextclade genotype calls as coloring in auspice 2. Set Nextclade genotypes as the default coloring 3. Use auspice config parameter naming and ordering schemes that match those of the Nextclade dataset tree, following changes made here: 07bf737
The changes made to the ingest workflow in a previous commit result in new columns of data being added to the metadata output of ingest. This commit adds those columns to the metadata of the example data in the phylogenetic workflow.
The nextclade dataset has now been released, and so we no longer need to point to the master version of the dataset server.
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Description of proposed changes
This PR does the following:
The Nextclade dataset is currently on the "master" version of Nextclade dataset server. After it is released, we can remove
--server=https://data.master.clades.nextstrain.org/v3from theget_nextclade_datasetrule.This PR addresses #32
Related issue(s)
#32
Checklist
--server=https://data.master.clades.nextstrain.org/v3from theget_nextclade_datasetrule after measles Nextclade dataset is released