Miscellaneous snakemake cleanup

[skoren]

• use extension smk instead of sm for syntax highlights on GitHub
• check the new feature that supports using existing bash scripts rather than inlining them in the smk files for cleaner smk files
• consider using https://github.com/snakemake/snakefmt to standardize formatting

[brianwalenz]

The script feature is described in snakemake/snakemake#1821 from Aug 22 and appears in release 7.14.0 from Aug 27. It requires bash, while verkko is happy with generic sh. It allows you to access the rule directives (input:, output:, etc) directly from the script. This would let us move the inlined shell scripts out of the Snakefiles and that could reduce the amount of escaping necessary. This would NOT let us stop generating scripts to run the task since the (external) script is useless without the snamemake variables passed to it.