Add Nextclade to ingest #7
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Add rules for running Nextclade as a part of the ingest workflow. These rules are optional because not every pathogen will have a Nextclade dataset to be able to run Nextclade as a part of ingest.
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The shell script for joining the metadata and Nextclade outputs is taken from @j23414's work in nextstrain/mpox#207 Co-authored-by: Jennifer Chang <[email protected]>
Stop hard-coding the expected `seqName` ID field used from Nextclade in case it get's renamed to something different in the user provided Nextclade column map.
Adds the default rule to rename the subset metadata TSV to the final metadata TSV if the Nextclade parameters are not defined in the config. This allows users to run the core ingest workflow with the simplest command of `nextstrain build .`
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I kept this PR open to make sure it aligned with changes made in nextstrain/mpox#207. |
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Description of proposed changes
Adds template for optional rules to run Nextclade as a part of the ingest workflow.
The Nextclade rules are optional because not every pathogen will have a Nextclade dataset to be able to run Nextclade as part of ingest.
This wraps up the "core" ingest workflow that produces the curated metadata and sequences.Maybe not, we should probably add Biosample data to the ingest template.