Issue in the MzTabExporter about mhcquant HOT 4 CLOSED

This usually indicates that the native ids in the annotated mzML file doesn't match to the native ids in the identification files.
The quantification looks sane to me @jpfeuffer? any idea:
https://github.com/nf-core/mhcquant/blob/master/subworkflows/local/post_quantification.nf
and it is run on the aligned files:
https://github.com/nf-core/mhcquant/blob/master/workflows/mhcquant.nf#L241-L250

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The problem is that this PeptideIdentification has an id_merge_index of 4 and a map_index of 0 this means that you are linking or otherwise merging quant. files (featureXMLs) that were annotated with IDs from multiple files.
In the new version we require a unique path back to the fragment spectrum in the mzml file.
This does not seem to be possible with how the workflow is constructed/parameterized. I won't have the time to look into the workflow before the weekend though I think.

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It might also be that one of the tools used was not updated yet to pass through information from merged ID files.

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I think that I found the problem, apparently, upstream not all of the individual files were given somehow which resulted in a conflict later on (trying to refer to an ID that was not available).

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