Add support for EPIC v2

[Nicklas Nordborg]

The EPIC methylation chip has come in a new version. The number of probes is different and there are several new probes and also many of the old ones that have been removed. Here is more information ​https://epicom.biomedcentral.com/articles/10.1186/s43682-023-00021-5

Our analysis depends on two files with metadata: EPIC.hg38.manifest.tsv and EPIC.hg38.mask.tsv. For the new chip version there are new files that should be used. We need to implement support for this in our pipeline so that it is possible to configure different metadata files (in reggie-config.xml) for different chips and to automatically select the correct files when creating the job script.

The current minfi (version 1.44) doesn't work with EPICv2. Execution ends with error message:

Error in .getManifestString(object@annotation) : 
  Cannot get Manifest object for an 'Unknown' array
Calls: preprocessRaw ... getProbeInfo -> getManifest -> getManifest -> .getManifestString
Execution halted
srun: error: cnl15: task 0: Exited with exit code 1

There seems to be a possible solution ​https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest

The container needs to be updated and our R script need some extra code.

[Nicklas Nordborg]

In 7509:

References #1558: Add support for EPIC v2

Changes to reggie-config.xml with configuration settings that depend on the chip type.

[Nicklas Nordborg]

In 7510:

References #1558: Add support for EPIC v2

Updated the BeadChipType annotation so it can be used on Methylation derived bioassays.

Renamed the Epic850K to EPICv1 and added EPICv2.

Annotations on existing annotation need to be updated or created manually with batch importers.

[Nicklas Nordborg]

In 7511:

References #1558: Add support for EPIC v2

Use the new configuration when starting jobs.