Job arrays across different wildcards may not create output directories

[ASLeonard]

Using snakemake v9.18 and slurm executor v2.6.

I have a rule that is wilcarded over a sample name and a "shard", which has a directory structure that depends on both wildcards. When using the new slurm jobarrays feature for ruleA, all jobs fail at the end because of missing output, and runs fine when not using the jobarray=ruleA arg.

rule ruleA:
    input:
        bam="{sample}.bam"
    output:
        vcf="finished/{sample}_{N}/test.vcf"

Given the warning about jobarrays and multiple wildcards, this seems likely to be the cause although I haven't had the chance to check if any directories are created while the jobarray is running.

[cmeesters]

Thanks for bringing this issue forward.

I am not sure: during implementation, I simplified the wildcard output for slurm logs, (as there is a common prefix for arrays, ordinarily). Other than that ... Hm, can you share the relevant snippet of a log / slurm log when running with --verbose?

Note, that I will be on holiday after Easter.