Move unrelated files out of Nextflow pipeline directory

[chasemc]

/Autometa/workflows/ is a Nextflow/nf-core specific directory, the following files should probably find another home. It may confuse future contributors

https://github.com/KwanLab/Autometa/blob/main/workflows/autometa-large-data-mode.sh
https://github.com/KwanLab/Autometa/blob/main/workflows/autometa.sh
https://github.com/KwanLab/Autometa/blob/main/workflows/autometa_flagged.sh

[evanroyrees]

Reminder: When these files are moved, any paths or links in the documentation will also need to be updated.