So, I made this simple Snakefile and I am wondering why my rule is interpreted as a localrule. Usually it's not a problem, but for my runs that need be submitted to SLURM it is. The only way I got it to work was writing the rule explicitly without wildcards. Then it was not interpreted as localrule. But then I obviously loose all the benefits of wildcards for my rules... I guess there is something I am missing here!
rule test:
output: "bla4_out.txt",
rule test_wild:
input: "bla{num}.txt",
output: "bla{num}_out.txt",
shell:
"""
touch {output}"
"""
This:
snakemake -n -R test
leads to
Building DAG of jobs...
Job stats:
job count min threads max threads
----- ------- ------------- -------------
test 1 1 1
total 1 1 1
[Mon May 9 13:02:41 2022]
localrule test:
output: bla4_out.txt
jobid: 0
resources: tmpdir=/tmp
Job stats:
job count min threads max threads
----- ------- ------------- -------------
test 1 1 1
total 1 1 1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.
If a rule doesn't have a directive that does something, like shell or run, then that rule is stamped as local. I guess it makes sense though... Try adding a dummy shell directive to your rule test and see what happens.