Checkpoint "get" still only resolvable once per aggregate function #3475
Description
Using an aggregate rule over the same checkpoint twice seems to only take the first occurrence. This seems similar to #3283, but does not seem fixed by #3341.
My use case here was splitting two VCFs with unknown samples, and then compare samples present in both files.
This code does not work, and you can tell something is wrong because snakemake will only complain if the "A.vcf" does not exist, but doesn't care if "B.vcf" doesn't exist, despite also being necessary input.
rule all:
input:
'A_B.csv'
checkpoint split_files:
input:
'{experiment}.vcf'
output:
directory('split_{experiment}')
rule happy:
input:
truth = 'split_{truth}/{sample}.vcf',
query = 'split_{query}/{sample}.vcf'
output:
'{truth}_{query}.{sample}.vcf'
shell: 'hap.py ...'
def aggregrate_happy(wildcards):
truth_samples = set(glob_wildcards(Path(checkpoints.split_files.get(experiment=wildcards.truth).output[0]).joinpath('{sample}.vcf')).sample)
query_samples = set(glob_wildcards(Path(checkpoints.split_files.get(experiment=wildcards.query).output[0]).joinpath('{sample}.vcf')).sample)
return [f'{wildcards.truth}_{wildcards.query}.{sample}.vcf' for sample in (truth_samples & query_samples)]
rule aggregate_happy:
input:
aggregrate_happy
output:
'{truth}_{query}.csv'
shell: 'cat {input} > {output}'
Generating two checkpoint rules or generating a second "fake" aggregate works
def aggregrate_happy(wildcards):
truth_samples = set(glob_wildcards(Path(checkpoints.split_files.get(experiment=wildcards.truth).output[0]).joinpath('{sample}.vcf')).sample)
return [f'{wildcards.truth}_{wildcards.query}.{sample}.vcf' for sample in truth_samples]
def fake_aggregate(wildcards):
query_samples = set(glob_wildcards(Path(checkpoints.split_files.get(experiment=wildcards.query).output[0]).joinpath('{sample}.vcf')).sample)
return []
rule aggregate_happy:
input:
aggregrate_happy,
fake_aggregate
So seems to be still limited to checkpoints.<rule>.get only being callable once per rule per function.
This was tested on versions v9.1.1 and v8.29.3.