Move generate_samplesheet to Python

[willbradshaw]

bin/generate_samplesheet.sh is a pretty elaborate script, probably too elaborate to be written in Bash rather than Python (or another language less awful than Bash). We should rewrite it.

[harmonbhasin]

Jeff just ran into an issue where the input directory was missing some of the reverse reads which was causing the script to fail. When we rewrite this script, we should make sure to have descriptive error messages.

[jeffkaufman]

Context: https://groups.google.com/a/securebio.org/g/nao-mu/c/UBzkf4IzbWk

[willbradshaw]

This need is getting pretty dire now; it's not quite top priority but we really should get it done sooner rather than later.

[harmonbhasin]

#155