feat: add file specific inputs/outputs for Snakefile

[strixy16]

run_readii rule in the Snakefile currently just checks for data/procdata/{DATASET_NAME}/images/readii_{DATASET_NAME} directory. Want it to check for the negative control specific files.

Notes

https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#data-dependent-conditional-execution
you would make the autopipeline rule a checkpoint then you can create an input function for another rule that parses the index file to generate all the files you want