Update pipeline document (#136)

* updated pipeline document

- standardized bismark output naming in parameter/output definitions
- added missing parameter definitions for all positional arguments
- added note about GeneLab suffix difference for DNA and RNA methylation
- removed bold formatting from files that are not output (trimming
  reports and gene-to-transcript map)
    - trimming report data is included in trimming multiqc report
    - gene-to-transcript map is part of reference generation and not study
    specific
- renamed deduplicated sorted output, alignment and bismark multiqc report output
- reconfigured MethylKit section to conform with output able format for other pipelines
    - Combined all pair-wise differential methylation analyses into one output table for 
       bases and one output table for tiles (without applying any significance cutoffs so data 
       from all regions are available), rather than providing multiple different files and only 
       providing differential methylation data for regions that meet significance cutoffs.
- added normalization step prior to differential methylation calculation
- replaced write.csv with data.table::fwrite for differential methylation output 
   tables for better write efficiency when these tables are large.
- reconfigure workflow_code folder
    - added isa_to_runsheet plugins folder
    - added runsheet spec
- add runsheet generation step
- add definition for dist.to.feature
- switch to using species instead of name column in annotations.csv
---------

Co-authored-by: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com>

Author: bnovak32

Methyl-Seq/Pipeline_GL-DPPD-7113_Versions/GL-DPPD-7113.md

@@ -0,0 +1,9 @@
+from pathlib import Path
+
+# Import for access at the module level
+from . import checks
+from . import protocol
+from . import schemas
+
+# Set config path
+config = Path(__file__).parent / "methylSeqDNA_v2.yaml"