feat(slurm-script): add reads support for combine

[mbhall88]

Summary

• pass the configured thread count to autocycler compress and autocycler trim
• provide the input reads and thread count to autocycler combine

Verification

• bash -n pipelines/Slurm_Autocycler_Bash_script_by_Michael_Hall/autocycler_slurm.sh
• git diff --check upstream/main...HEAD
• cargo build --verbose
• cargo test --verbose (187 passed)

[rrwick]

Thanks for keeping your script updated!