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Refactor workflows to follow Nextstrain standards from ncov workflow #58
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enhancement
New feature or request
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Bumping this issue because we were asked during Nextstrain office hours (Oct 7, 2021) if we have plans to create a flu workflow similar to the ncov template/tutorial. |
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Context
In the near future, we would like to support region-specific flu builds and also enable other researchers to use this repository to define their own custom flu builds in the same way the ncov repository allows custom workflows.
Description
Seasonal flu builds should follow the same general pattern as ncov builds where a standard workflow depends on an initial selection of sequences (based on some subsampling logic), inferring and annotating phylogenies, and then running build-specific steps to finalize the analysis.
Users should be able to configure their own workflows by modifying configuration files (e.g., YAML or JSON) and/or defining custom Snakemake profiles.
Existing parallel Nextstrain builds ("live" and "WHO") should be executable through this framework, such that we are users of our own workflow configuration system.
Examples
See Nextstrain's ncov regional builds definitions for a real example of what we would like to support for flu eventually.
Possible solutions
Specific solutions will require more discussion, but the basic first steps toward addressing this issue would be similar to what we had to do for ncov back in March/April:
workflow/*.smk
files including acommon.smk
for shared functions andbuilds.smk
for the main build logic.The text was updated successfully, but these errors were encountered: