Move hardcoded parameters to the config file

[j23414]

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)

• phylo: Move hardcoded params to config YAML #35

Checklist

• Checks pass

[j23414]

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

zika/phylogenetic/rules/construct_phylogeny.smk

Lines 64 to 68 in f2c287a

	--timetree \
	--coalescent {params.coalescent} \
	--date-confidence \
	--date-inference {params.date_inference} \
	--clock-filter-iqd {params.clock_filter_iqd}

Or perhaps put them into one combined refine args config?

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

[joverlee521]

Thanks for following up here, changes look good to me!

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

I don't think so. The current refine config parameters only make sense when used with the --treetime flag.

In general, I don't think we want to go down the road of making every flag parameterized. That was just unsustainable in the ncov workflow...