bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs

I usually remove Ns from the sample sheet and then run this command

$ bcl2fastq -i Runfolder/Data/Intensities/BaseCalls -R Runfolder -o output_directory --sample-sheet Runfolder/SampleSheet.csv -r number_of_threads -p number_of_threads -w number_of_threads --no-lane-splitting --mask-short-adapter-reads 0 --use-bases-mask Y*,I8Y9,I8,Y*

Original sample sheet:

Sample_ID,Sample_Name,Description,index,I7_Index_ID,index2,I5_Index_ID,Sample_Project
Sample1,Sample1,,TACCGAGGNNNNNNNNN,TACCGAGGNNNNNNNNN,AGTTCAGG,AGTTCAGG,BRCA1
Sample2,Sample1,,CGTTAGAANNNNNNNNN,CGTTAGAANNNNNNNNN,GACCTGAA,GACCTGAA,BRCA1

Formatted sample sheet:

Sample_ID,Sample_Name,Description,index,I7_Index_ID,index2,I5_Index_ID,Sample_Project
Sample1,Sample1,,TACCGAGG,TACCGAGG,AGTTCAGG,AGTTCAGG,BRCA1
Sample2,Sample1,,CGTTAGAA,CGTTAGAA,GACCTGAA,GACCTGAA,BRCA1

Our RunInfo.xml file looks like this:

<Reads>
      <Read Number="1" NumCycles="147" IsIndexedRead="N" />
      <Read Number="2" NumCycles="17" IsIndexedRead="Y" />
      <Read Number="3" NumCycles="8" IsIndexedRead="Y" />
      <Read Number="4" NumCycles="146" IsIndexedRead="N" />
    </Reads>