Use default config and partial overrides #173
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Previously, either config_hmpxv1.yaml was used as the default as-is or all required configuration were to be specified via Snakemake CLI options. This resulted in much duplication of configuration across different usages, and the default was never actually used in practice except for in CI out of convenience of not specifying --configfile. Switch to a two-tiered configuration setup with (1) a base "default" tier of common values that can be applied to all workflow usages and (2) a second tier of usage-specific config values which can also partially override Since some required config entries (e.g. build_name) do not share common values across the existing configs, this results in a workflow that is only usable when additional configuration is defined. This will be addressed by subsequent commits.
Copy values from the hmpxv1 configuration since that was the previous default, but change the names to be boilerplate defaults. Add required entries so that: 1. The default config file serves as a reference for all required keys. 2. The workflow can be run by CI without specifying an additional --configfile.
4 tasks
joverlee521
approved these changes
Aug 22, 2023
1 task
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Hmm, I don't like having an extra default config file which makes it more difficult to trace where a particular config value comes from. PR #171 reworks things a little anyways. I'll add a default profile which specifies a default config file so things can be run as |
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Description of proposed changes
Refactoring the way Snakemake configuration is handled in this workflow to be more consistent with the ncov workflow.
Related issue(s)
Testing