When `maxRetries > 0`, and the job fails, the cli_log is overwritten, hiding useful error messages

[hexylena]

Hi! I noticed recently when I had a job fail, and I went looking for the reason, that the cli_log:

miniwdl/WDL/runtime/backend/cli_subprocess.py

Lines 70 to 71 in 6ecfc6f

	cli_log_filename = os.path.join(self.host_dir, f"{self.cli_name}.log.txt")
	cli_log = cleanup.enter_context(open(cli_log_filename, "wb"))

is overwritten by default. Here is the current state of a workflow:

$ ls analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/std*
analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/stderr2.txt
analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/stdout2.txt
analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/stderr.txt
analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/stdout.txt

$ ls analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/slurm_singularity*
analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/slurm_singularity.log.txt

$ cat analysis/02-lrrnaseq/20250616_095354_LongReadRnaSeq/call-flairCollapse/slurm_singularity.log.txt 
srun: job 21258585 queued and waiting for resources

$

It would be nice if the cli_log could either be appended to, or use a numeric suffix like

Here's the relevant portion of my miniwdl.cfg:

[task_runtime]
defaults = {
        "maxRetries": 2,
        "threads": 4,
        "docker": "ubuntu:20.04"
    }

It is indeed slurm (via the https://github.com/miniwdl-ext/miniwdl-slurm) and I could find out why the job failed via my DRM, but in general it would be nice to not overwrite the log.

Perhaps this is as simple as change w for a in the logger, but perhaps there's a nice way to do the numerical append like with stdout/err so I can keep a good association between them

Thanks for the consideration

[mlin]

Yea where SubprocessBase formulates cli_log_filename it should incorporate its base class' TaskContainer.try_counter similarly to how it's used in the std{out,err}.txt filenames.