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Snakemake simplifications #72
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a8bf1c3
multi-threaded alignment & tree building
jameshadfield eb7c363
refactor some inputs to functions
jameshadfield aef6d75
Segment builds for H5N1 cattle flu outbreak
jameshadfield beb0275
Update filenames for h5n1-cattle-flu segments
jameshadfield d60bfca
Refactor clock-rate params
jameshadfield f44ad6c
Merge snakemake.genome into main pipeline
jameshadfield 88ffb8c
Use config YAMLs
jameshadfield b5f84e2
Integrate common.smk into Snakefile
jameshadfield 6ba46b5
Refactor input filenames
jameshadfield ff3b2ab
Organise results into directories
jameshadfield f37a038
Add hierarchy to config directory
jameshadfield 0f0d6d0
Export h5_label_clade for h5n1-cattle-outbreak
jameshadfield cfefd2d
Update GitHub Actions invocations
jameshadfield ab3ef2e
[phylo github actions] add summary message
jameshadfield e6b9158
Run h5n1-cattle-outbreak builds on AWS Batch
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FYI, a similar update will need to be applied to docker-base, conda-base, and augur CI workflows.
I am considering if we want to use
config/gisiad.yaml
as a default config. Then we wouldn't need to update the build-args in CI and we can keep the simplenextstrain build
invocation without needing to provide a config file.This can be done in two ways:
The downside to this method is the config dictionaries merge. This becomes an issue when adding
--configfile config/h5n1-cattle-outbreak.yaml
, as the top levelbuilds
would merge and run all subtypes.The config dictionary merge issue from [1] still exists, but at least this way adding
--configfile config/h5n1-cattle-outbreak.yaml
will completely switch over to the h5n1-cattle-outbreak config params. The downside to this method is users need to remember to provide the configfile if they want to override specific configs with--config
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Urgh. Thanks for noticing - this would have been a pain to solve post-merge!
I like the explicitness of providing a
--configfile
for each run. But do I like it enough to make changes across 3 extra repos? Probably. Will think about it some more.There was a problem hiding this comment.
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(Only noticed because we recently went through this in #17).
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PRs made to update CI in