Ingest with nextclade #62
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joverlee521
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Motivated by my own need to test the ingest workflows for the latest addition of Nextclade outputs in #62.
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Using `community/moncla-lab/iav-h5/ha/all-clades` as the default Nextclade dataset since it works across fauna and NCBI data. Subsequent commits will join these rules with the full ingest workflows.
Using the nextclade_field_map that's currently used in the measles ingest workflow.¹ We can cut down on the columns used if they are not useful for avian flu. ¹ <https://github.com/nextstrain/measles/blob/957fc744c64b8f5a722b5c525687d0746755add6/ingest/defaults/nextclade_field_map.tsv>
We are not using the alignment.fasta anywhere and I don't think it makes sense to only upload alignment for the HA segment.
Keep a copy of the full Nextclade TSV output from ingest on S3 since we won't necessarily join all columns with the metadata output.
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joverlee521
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Jun 24, 2024
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| coverage coverage | ||
| totalMissing missing_data | ||
| totalSubstitutions divergence | ||
| totalNonACGTNs nonACGTN | ||
| qc.overallStatus QC_overall | ||
| qc.missingData.status QC_missing_data | ||
| qc.mixedSites.status QC_mixed_sites | ||
| qc.privateMutations.status QC_rare_mutations | ||
| qc.snpClusters.status QC_snp_clusters | ||
| qc.frameShifts.status QC_frame_shifts | ||
| qc.stopCodons.status QC_stop_codons | ||
| frameShifts frame_shifts | ||
| privateNucMutations.reversionSubstitutions private_reversion_substitutions | ||
| privateNucMutations.labeledSubstitutions private_labeled_substitutions | ||
| privateNucMutations.unlabeledSubstitutions private_unlabeled_substitutions | ||
| privateNucMutations.totalReversionSubstitutions private_total_reversion_substitutions | ||
| privateNucMutations.totalLabeledSubstitutions private_total_labeled_substitutions | ||
| privateNucMutations.totalUnlabeledSubstitutions private_total_unlabeled_substitutions | ||
| privateNucMutations.totalPrivateSubstitutions private_total_private_substitutions | ||
| qc.snpClusters.clusteredSNPs private_snp_clusters | ||
| qc.snpClusters.totalSNPs private_total_snp_clusters |
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Should we only keep the clade assignment and drop all of these other columns? These QC outputs are specific to the HA segment so it might not make sense to keep as part of the overall metadata.
genehack
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Jun 24, 2024
joverlee521
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Jun 24, 2024
| # Nextclade can have pathogen specific output columns so make sure to check which | ||
| # columns would be useful for your downstream phylogenetic analysis. | ||
| seqName seqName | ||
| clade clade |
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Would it make sense to include the polybasic_cleavage_site output column or should the phylogenetic builds continue to rely on scripts/annotate-ha-cleavage-site.py?
joverlee521
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Jun 24, 2024
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| { | ||
| "key": "clade", | ||
| "title": "Nextclade Clade", | ||
| "type": "categorical" | ||
| }, |
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I've added the Nextclade Clade as a separate coloring so we can do comparisons across clade labels, but maybe we'll remove h5_label_clade eventually? Would love to hear your thoughts here @lmoncla 🙏
genehack
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Jun 26, 2024
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Description of proposed changes
Runs Nextclade as part of the ingest workflow so that we get Nextclade clade annotations for all H5 HA sequences.
Uses the
community/moncla-lab/iav-h5/ha/all-cladesNextclade dataset.Related issue(s)
Resolves #44
Checklist
-> results at
s3://nextstrain-data-private/files/workflows/avian-flu/trial/ingest-with-nextclade/metadata.tsv.zsts3://nextstrain-data/files/workflows/avian-flu/trial/ingest-with-nextclade/h5n1/metadata.tsv.zst