--delete-all-output ignores --dry-run #3264
Description
Snakemake version
8.27.1
Describe the bug
Running --delete-all-output with --dry-run ignores dry-run, it deletes all output files.
Logs
Minimal example
Snakefile:
rule all:
input:
expand("results/{name}.txt", name=range(2))
rule A:
output:
"results/{name}.txt"
shell:
"touch {output}"
Command-line:
$ snakemake -c1
Assuming unrestricted shared filesystem usage.
host: bif02.ircm.priv
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
----- -------
A 2
all 1
total 3
Select jobs to execute...
Execute 1 jobs...
[Wed Jan 22 14:53:35 2025]
localrule A:
output: results/0.txt
jobid: 1
reason: Missing output files: results/0.txt
wildcards: name=0
resources: tmpdir=/tmp
[Wed Jan 22 14:53:35 2025]
Finished job 1.
1 of 3 steps (33%) done
Select jobs to execute...
Execute 1 jobs...
[Wed Jan 22 14:53:35 2025]
localrule A:
output: results/1.txt
jobid: 2
reason: Missing output files: results/1.txt
wildcards: name=1
resources: tmpdir=/tmp
[Wed Jan 22 14:53:35 2025]
Finished job 2.
2 of 3 steps (67%) done
Select jobs to execute...
Execute 1 jobs...
[Wed Jan 22 14:53:35 2025]
localrule all:
input: results/0.txt, results/1.txt
jobid: 0
reason: Input files updated by another job: results/1.txt, results/0.txt
resources: tmpdir=/tmp
[Wed Jan 22 14:53:35 2025]
Finished job 0.
3 of 3 steps (100%) done
Complete log: .snakemake/log/2025-01-22T145335.409725.snakemake.log
Dry-run delete all output:
$ snakemake -c1 --dry-run --delete-all-output
Building DAG of jobs...
Deleting results/0.txt
Deleting results/1.txt
All files have been deleted instead of listing the files that would be deleted.
Additional context
The issue comes from:
cli.py lines 2151-2154
We can see that just adding dag_api.delete_output(dryrun=args.dryrun) like in delete_temp_output should fix the issue. I can open a PR with a fix if you would like.