Fixup config syntax #146
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Fixup config syntax #146
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joverlee521
approved these changes
Mar 6, 2025
rules/config.smk
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| the subtype query value does not vary across segment or time wildcards. | ||
| """ | ||
| def resolve(wildcards): | ||
| return resolve_config_value('subtype_query')({"subtype": wildcards.subtype, 'segment': '*', 'time': '*'}) |
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Good to know that this enforces that the subtype_query must be <subtype>/*/*.
When I tried modifying the config to
subtype_query:
"h5n1-cattle-outbreak/ha/*": "genoflu in 'B3.13'"
I get the following error:
$ nextstrain build . -s genome-focused/Snakefile -n
Building DAG of jobs...
InputFunctionException in rule filter_sequences_by_subtype in file /nextstrain/build/genome-focused/../rules/main.smk, line 179:
Error:
InvalidConfigError: Config structure incorrect or incomplete for config["subtype_query"]
The dictionary is missing a matching key for the current target of 'h5n1-cattle-outbreak/*/*', or a fuzzy match (i.e. using "*" placeholders)
P.S. If you want to use a single value across all builds then set a scalar value (number, string, boolean)
Wildcards:
subtype=h5n1-cattle-outbreak
segment=pb2
Traceback:
File "/nextstrain/build/genome-focused/../rules/config.smk", line 261, in resolve
File "/nextstrain/build/genome-focused/../rules/config.smk", line 147, in resolve
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Relatedly, I want (wanted?) to change the workflow for the genome builds such that (conceptually) each segment had a different subtype query, kind of like you've tried here, but it required too much snakemake surgery so I kicked it down the road. This would be useful for us because, e.g., the B3.13 constellation is PB2:am2.2, PB1:am4, ... so we could build the avian-flu/h5n1-cattle-outbreak/pb2 tree filtering to am2.2 and the entire genome tree filtering to B3.13
Brings the config structure in line with all of the other config values, but this necessitates a more complicated usage of `resolve_config_value`. Hopefully the added comments are instructive to people in the future! This also greatly improves the error handling if we forget to add the appropriate subtype to the config, or leave out 'subtype_query' altogether. Inspired by <#104 (comment)> and <#146 (comment)>
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Little improvements identified in post-merge review of #104