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.

[Nicklas Nordborg]

In 7512:

References #1558: Add support for EPIC v2

Updated the container definition with additional software that is needed for EPICv2 support.

Minfi has been updated to version 1.48.

[Nicklas Nordborg]

In 7513:

References #1558: Add support for EPIC v2

Export the BeadChipType annotation and make it available in the R script.

[Nicklas Nordborg]

In 7514:

References #1558: Add support for EPIC v2

Changes to the beta-value script that are related to the EPICv2 support.

• We need to set annotations on the mIdat object so that they are not 'Unknown'.
• Columns in the MASK file have different names: Probe_ID instead of probeId and M_general instead of MASK_general.
• Another big difference is that the mask file only list probes with some kind of filter (about 10%) so the part that filters out masked probes needed a different strategy.

[Nicklas Nordborg]

In 7516:

References #1558: Add support for EPIC v2

The BeadChipPosition annotation has been enabled for use on Methylation items.

[Nicklas Nordborg]

In 7517:

References #1558: Add support for EPIC v2

Use BeadChipPosition from the Methylation item instead of from the DNA aliquot.

[Nicklas Nordborg]

In 7518:

References #1558: Add support for EPIC v2

Updated reggie-config.xml to use the new container.