nextstrain/ncov

Define workflow dependencies

victorlin opened this issue · 0 comments

victorlin commented

Context

This workflow only works with specific versions of software. There is a Conda environment file (workflow/envs/nextstrain.yaml) however this has issues:

  1. It is only meant for use within Snakemake (--use-conda, rule.conda)
  2. It acts more like a "lock" file with exact version pins
  3. It doesn't document the version constraint on Snakemake (the workflow doesn't support Snakemake 8.x)

Proposal

  1. Create a list of workflow dependencies as supported ranges. Drafting that here:

    • Augur: >= 22.0.1 (ref)
    • Snakemake: ?? <= 8.0.0
    • ?

  2. Check at the start of running the workflow. This is what's already done in other workflows such as nextstrain/mpox@d9f6d47

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