Localrules are ignored for grouped jobs

I am using the latest versions of snakemake (8.25) and am trying to use the executor plugin (0.11.1) for slurm for my pipeline. However, when I use the command-line to run snakemake with the slurm executor all rules are considered SLURM-rules. That is to say, neither localrules: a, b, c nor the per-rule localrule: True directive have any effect. After some digging I found that this only occurs if the group directive is used on the respective rules. I.e. if I remove the grouping then everything runs fine and localrules are recognized properly.

Minimal Snakefile if you want to try it

The rule a belongs to group local


DIRECTORY = "test"

rule all_a:
    input: 
        [f"{DIRECTORY}/test_file-a-{i}.txt" for i in range(10)],
    localrule: True

rule a:
    input: 
        directory(DIRECTORY)
    output:
        DIRECTORY + "/test_file-a-{i}.txt"
    localrule: True
    group:
        "local"
    shell:
        "touch {output[0]}"

Running all_a reveals that both all_a as well as a are considered normal rules rather than localrules

$ snakemake --executor slurm -R all_a

Job stats:
job      count
-----  -------
a           10
all_a        1
total       11

Select jobs to execute...
Execute 10 jobs...

[Fri Nov  1 13:57:51 2024]
rule a:
    input: test
    output: test/test_file-a-4.txt
    jobid: 5
    reason: Missing output files: test/test_file-a-4.txt
    wildcards: i=4
    resources: mem_mb=<TBD>, disk_mb=<TBD>, tmpdir=<TBD>, slurm_account=<TBD>

[Fri Nov  1 13:57:51 2024]
rule all_a:
    input: test/test_file-a-0.txt, test/test_file-a-1.txt, test/test_file-a-2.txt, test/test_file-a-3.txt, test/test_file-a-4.txt, test/test_file-a-5.txt, test/test_file-a-6.txt, test/test_file-a-7.txt, test/test_file-a-8.txt, test/test_file-a-9.txt
    jobid: 0
    reason: Forced execution
    resources: mem_mb=<TBD>, disk_mb=<TBD>, tmpdir=<TBD>, slurm_account=<TBD>

on the other hand if we remove the group clearative and run the same command in the terminal we get:

$ snakemake --executor slurm -R all_a

Job stats:
job      count
-----  -------
a           10
all_a        1
total       11

Select jobs to execute...
Execute 10 jobs...

[Fri Nov  1 14:05:23 2024]
localrule a:
    input: test
    output: test/test_file-a-4.txt
    jobid: 5
    reason: Missing output files: test/test_file-a-4.txt
    wildcards: i=4
    resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/tmp, slurm_account=bczk-delta-gpu

[Fri Nov  1 14:05:23 2024]
localrule all_a:
    input: test/test_file-a-0.txt, test/test_file-a-1.txt, test/test_file-a-2.txt, test/test_file-a-3.txt, test/test_file-a-4.txt, test/test_file-a-5.txt, test/test_file-a-6.txt, test/test_file-a-7.txt, test/test_file-a-8.txt, test/test_file-a-9.txt
    jobid: 0
    reason: Forced execution
    resources: mem_mb=1000, mem_mib=954, disk_mb=1000, disk_mib=954, tmpdir=/tmp, slurm_account=bczk-delta-gpu

indicating that now the rules are indeed localrules.

PS: as you can probably see from the copy/paste output, the actual commands used also specified some resources and partitions which is actually how I found the bug in the first place as I was trying to run simple CPU stuff on a GPU partition since SLURM is only supposed to be used by gpu-using rules in my pipeline...

Thanks a lot already,

Cheers, Noah :sunny:

snakemake / snakemake-executor-plugin-slurm

Localrules are ignored for grouped jobs #162

Minimal Snakefile if you want to try it