Is your feature request related to a problem? Please describe.

Currently, the properties injected into the jobscript include input and output

When running a job that has thousands of input or output files this creates a problem on slurm. Slurm's default script size if 4MB. I have an example of a job that takes 44,000 input files and the jobscript is 4.6MB. As such, it fails submission to slurm.

Describe the solution you'd like

Do input and output need to be in the properties injected into the jobscript? The slurm and lsf profiles dont use these properties, is there other things using it?

If not, can we just remove them?

Additional context

This has arisen in the slurm profile before also - see Snakemake-Profiles/slurm#87