SciLifeLab/Sarek: Sarek 2.0.0

CAW is dead, long live Sarek!! With this new version, a change of name. The main script is now separated into five different scripts. So there is obviously some minor changes for executing the workflow. But apart from that, it's the same pipeline it was before.

• basic wrapper script
• Abstract, posters and figures
• ROI selector and FreeBayes sanitizer scripts
• New logo and icon for the project
• check for existing tumor/normal channel
• lib/SarekUtils.groovy with checkParams, checkParameterList, checkParameterExistence and isAllowedParams functions
• some runOptions for docker (prevent some user right problem)
• This CHANGELOG

• CAW is now Sarek
• Dissect Workflow in 5 new scripts: annotate.nf, main.nf, germlineVC.nf, runMultiQC.nf and somaticVC.nf
• report.html, timeline.html and trace.html are generated in Reports/
• --version is now used to define the workflow version
• most params are now defined in the base.config file instead of in the scripts
• update RELEASE_CHECKLIST.md
• checkParams, checkParameterList, checkParameterExistence and isAllowedParams in script functions are now called within SarekUtils
• nf_required_version is now params.nfRequiredVersion
• in buildReferences.nf script, channels now begin by ch_, and files by f_
• use PublishDir mode: 'link'`` instead ofcopy`
• directoryMap now contains params.outDir
• use Nextflow support of scratch (close #539)
• reordered Travis CI tests
• update documentation
• MultiQC version in container from v1.4 to v1.5
• vepgrch37 container base image from release_90.6 to release_92
• vepgrch38 container base image from release_90.6 to release_92
• VEP version in containers from v90 to v91
• nucleotidesPerSecond is now params.nucleotidesPerSecond
• default params.tag is now latest instead of current version, so --tag needs to be specified with the right version to be sure of using the containers corresponding

• standard profile
• uppmax-localhost.config file

• scripts/skeleton_batch.sh
• old data and tsv files
• UPPMAX directories from containers
• --step in annotate.nf, germlineVC.nf and somatic.nf
• some runOptions for Singularity (binding not needed anymore on UPPMAX)
• download profile

• Replace VEP --pick option by --per_gene (fix #533)
• use $PWD for default outDir (fix #530)