Add Singularity support

Upgrade to Snakemake 5.9.1, which has fixes to Singularity support.

Add loading of Singularity module.

Add checking for 'singularity:' directives to snakemakeslurm warning system.

Add '--use' which auto-generates --use-conda and/or --use-singularity when those directives appear in the Snakefile.