Fix log report for non-bash output

[Headonpillow]

Add proper logging to R scripts.

Summary — approach

• Tell each script to write its console output (stdout + messages) to the Snakemake log file when run under Snakemake. Use the Snakemake-provided log handle (snakemake@log in R, snakemake.log in Python).

• Add informative messages (using message() / cat() in R, logging in Python) at important events: samples read, duplicates removed, numbers filtered/retained, ASV counts, files written, any warnings/errors.

• Keep behavior unchanged when run interactively (the scripts still error if run without Snakemake), but when run by Snakemake the logs will contain the R console output and the specific informative statements.

Keep in mind:
Snakefile already creates log files.