* rules/bio/ngs/methylseq/bismark.rules: add rules align, deduplicate, methXtract for entire bismark pipeline
* rules/bio/ngs/methylseq/bismark.rules: correct bismark_align so read1, read2 file used as input and not read1, read1
* rules/bio/ngs/settings.rules: add read1, read2 suffix specification for pathological renaming cases
Merge branch 'develop' into feature/methylseq

Conflicts:
	rules/bio/ngs/methylseq/bismark.rules
Fixed
Merge branch 'develop' into feature/methylseq
Merge branch 'develop' into feature/methylseq
* rules/bio/ngs/methylseq/bismark.rules: Update rules
Merge remote-tracking branch 'refs/remotes/origin/develop' into feature/methylseq

Conflicts:
	rules/bio/ngs/methylseq/bismark.rules
Finish merge
updates to bismark; add methylation workflow
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
* rules/bio/ngs/methylseq/bismark.rules: add suffix labels for finding input
* rules/bio/ngs/qc/picard.rules: move find_merge_inputs; add inputfun key
* workflows/bio/methylseq.workflow: add configuration items. Reimplement alignment step as here we take trim_galore as input.
Merge branch 'feature/methylseq' into develop