Move hardcoded parameters to the config file

nextstrain / zika

Nextstrain build for Zika virus

https://nextstrain.org/zika

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Move hardcoded parameters to the config file #48

Closed j23414 closed 4 months ago

j23414 commented 4 months ago

Description of proposed changes

Updates the phylogenetic workflow to set hardcoded parameters through the default config YAML. This will make it easier for users to override default values.

Related issue(s)

https://github.com/nextstrain/zika/issues/35

Checklist

[ ] Checks pass

j23414 commented 4 months ago

Clarification question, did we also want to move hardcoded flags (e.g. --treetime and --date-confidence) into a config YAML?

https://github.com/nextstrain/zika/blob/f2c287aa720c7708ce097c48dccc3a06bda75964/phylogenetic/rules/construct_phylogeny.smk#L64-L68

Or perhaps put them into one combined refine args config?

refine:
  coalescent: "opt"
  date_inference: "marginal"
  clock_filter_iqd: 4
  args: "--treetime --date-confidence"