More fixes and enhancements for 2.0.0

[maxulysse]

• remove UPPMAX directories from containers
• --version is now used to define the version of the workflow
• move version to base.config within the params --version
• update RELEASE_CHECKLIST.md
• add lib/SarekUtils.groovy
• move checkParams, checkParameterList, checkParameterExistence and isAllowedParams functions into SarekUtils
• nfRequiredVersion is now a params
• in buildReferences.nf channels now begin by ch_, and files by f_
• use PublishDir mode: 'link' instead of copy
• use $PWD for default outDir to fix No results are copied to any output directory #530
• directoryMap now contains params.outDir
• use Nextflow support of scratch to close Use Nextflow support for /scratch instead of running directly from /scratch #539
• update documentation
• add CHANGELOG

[ewels]

Nice, very tidy! Maybe better to call SarekUtils instead of MyUtils though, so that it's clearer in main.nf?

[maxulysse]

Good idea