* rules/bio/ngs/qc/picard.rules: Updated commands to comply with new GATK-like picard. Add function to collect input files to merge sam.
* rules/bio/ngs/qc/picard_old.rules: Old-style picard rules.
* rules/bio/ngs/qc/picard.rules: update bam finding function
* workflows/bio/variation.workflow: add numerous functions
* rules/bio/ngs/tools/gatk.rules: add filtering and select rules
updates to bismark; add methylation workflow
* rules/bio/ngs/settings.rules: remove trailing BaseConfig

* rules/bio/ngs/variation/variation.rules: fix snpeff command. Comment out annovar download rules for now as they trigger errors
* workflows/bio/variation.workflow: update
Merge branch 'feature/variantcallingworkflow' into develop
Merge remote-tracking branch 'refs/remotes/origin/develop' into feature/methylseq
Merge remote-tracking branch 'refs/remotes/origin/develop' into feature/methylseq
Merge remote-tracking branch 'refs/remotes/origin/feature/methylseq' into develop