DSL2 update

Update to Nextflow DSL2 and add code to generate genotype matrix for cross object for RILs

Original pipeline release

Mostly written by DEC (<2018) with few minor updates from DL (Dec 2020). This is a stable version of the pipeline that uses Nextflow DSL1 and a docker container to run. This version can be run remotely with nextflow run andersenlab/nil-ril-nf -r v1.0 ...