Changes between Initial Version and Version 4 of Ticket #1558


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Timestamp:
Dec 15, 2023, 8:09:52 AM (5 months ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1558 – Description

    initial v4  
    22
    33Our 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.
     4
     5The current minfi (version 1.44) doesn't work with EPICv2. Execution ends with error message:
     6
     7{{{
     8Error in .getManifestString(object@annotation) :
     9  Cannot get Manifest object for an 'Unknown' array
     10Calls: preprocessRaw ... getProbeInfo -> getManifest -> getManifest -> .getManifestString
     11Execution halted
     12srun: error: cnl15: task 0: Exited with exit code 1
     13}}}
     14
     15There seems to be a possible solution https://github.com/jokergoo/IlluminaHumanMethylationEPICv2manifest
     16
     17The container needs to be updated and our R script need some extra code.