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@mraves2 mraves2 commented Jul 11, 2025

The PeakFinding step in the DIMS pipeline has been refactored. Instead of averaging the intensities for technical replicates and doing PeakFinding on the averages, the new method will do PeakFinding for each technical replicate. To do this, several scripts have been modified:

  • DIMS.nf:
    • AverageTechReplicates: averaging part removed, script renamed to EvaluateTics
    • extra step AveragePeaks after PeakFinding added
    • extra step CollectAveraged after AveragePeaks added
    • extra channel with information which technical replicates belong to which biological sample
    • PeakGrouping input from CollectAveraged
    • SpectrumPeakfinding step has been removed
  • DIMS.config:
    • AverageTechReplicates step replaced by EvaluateTics
    • extra step CollectAveraged added

@mraves2 mraves2 marked this pull request as draft July 11, 2025 15:40
@mraves2 mraves2 marked this pull request as ready for review July 17, 2025 13:41
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3 participants