Update template workflows to support separate analysis directory

[joverlee521]

Copied from parent issue

Running workflows from a separate analysis directory

There are prototypes of this here and here, and the corresponding CLI prototype is here. Once these prototypes have solidified I expect the necessary snakemake modifications will be added to this guide. While they still require the workflow repo directory to be managed by the user (git cloned, updated etc), I think that's enough for the purposes of this goal; if we can get the CLI to manage them then even better.

[joverlee521]

Sharing current WIP.

0995778 adds a shared resolve_config_path function, which is built on the work @tsibley did in measles and the work @jameshadfield did in avian-flu. It optionally takes a wildcards param that can be used to expand the path with Snakemake wildcards so that it can work for both single build workflows and multi-build workflows.

Experimenting vendoring this function across pathogen repos with Snakemake modules in measles. nextstrain/measles@f038991 fetches the shared resolve_config_path function from pathogen-repo-guide and nextstrain/measles@c7d5053 updates the phylogenetic workflow to use wildcards for config file paths.

[tsibley]

Added two quick comments on the WIP code.

1. nextstrain/measles@c7d5053#r156194449
2. 0995778#r156194598

[jameshadfield]

@joverlee521 - have you tried the code in https://github.com/nextstrain/shared/ in avian-flu? When I was reading it today it struck me that it would be good to have both avian-flu & measles WIP branches which use the code in shared (either vendored or copy-pasted). Happy to help on the avian-flu side

[joverlee521]

@joverlee521 - have you tried the code in https://github.com/nextstrain/shared/ in avian-flu? When I was reading it today it struck me that it would be good to have both avian-flu & measles WIP branches which use the code in shared (either vendored or copy-pasted). Happy to help on the avian-flu side

Thank @jameshadfield! Adding the vendored code to avian-flu is definitely part of the plan. I was trying it out locally but just didn't clean it up to push to a WIP branch yet.

[joverlee521]

Okay latest progress

• see resolve_config_path in nextstrain/shared
• Using the vendored function
  • Use vendored shared functions measles#60
  • Use vendored shared functions avian-flu#150

If this all looks reasonable, then I'll update the pathogen-repo-guide with the same vendored function.