Fix snakemake rule existence checks #1084
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
trvrb
approved these changes
Sep 20, 2023
tsibley
requested changes
Sep 20, 2023
We use the existence of certain rules to control the DAG and the way rules are stored internally changed in snakemake 7.32.1 <snakemake/snakemake@65c79a4> This functionality is (probably?) only used for internal nextstrain builds where we use the `auspice_config` rule to programmatically generate the config.
jameshadfield
force-pushed
the
fix/snakemake-7.32.1
branch
from
34839d1 to
0279181
Compare
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
We use the existence of certain rules to control the DAG and the way rules are stored internally changed in snakemake 7.32.1 snakemake/snakemake@65c79a4
This functionality is (probably?) only used for internal nextstrain builds where we use the
auspice_configrule to programmatically generate the config.On 2023-09-14 we updated snakemake from 7.24.1 to 7.32.3 in our docker image. This caused our nCoV builds to (incorrectly) use the default auspice-config JSON rather than call the
auspice_configrule to generate it. This can be seen by comparing the datasets from Sept 12th and Sept 15th