Documentation error: incorrect varible name in example for lookup() #3541
Description
Snakemake version
# snakemake --version
9.3.0
Describe the bug
The example code for the lookup() function in the Snakemake documentation uses the variable sample when it should be item.
In the Snakemake documentation at "Snakefiles and Rules"->"Helpers for defining rules"->"Semantic helpers"->"The lookup function", the example code...
collect("results/{item.sample}.txt", sample=lookup(query="someval > 2", within=samples))
...produces a WildcardError... No values given for wildcard 'item'. error.
The example code should be...
collect("results/{item.sample}.txt", item=lookup(query="someval > 2", within=samples))
Logs
With current example code:
# snakemake --cores=1 --force
WildcardError in file "/Users/jason/dev/learn/snakemake/learn/Snakefile", line 13:
No values given for wildcard 'item'.
Minimal example
# mkdir results
# touch results/{a,b,c}.txt
# cat Snakefile
import pandas as pd
samples = pd.DataFrame.from_records(
(
{"sample": "a", "someval": 4},
{"sample": "b", "someval": 2},
{"sample": "c", "someval": 8},
),
)
rule test_rule:
input:
collect("results/{item.sample}.txt", sample=lookup(query="someval > 2", within=samples))
output:
"output/sample_list"
shell:
"""
echo \\# $(date) > {output}
echo The input files captured are... >> {output}
echo '{input}' >> {output}
"""