I have bcl files from 10X genomics and trying to demultiplex them and generate fastq files. to do so, I m using cellranger mkfastq and once I have fastq files I will use cellranger multi. for the cellranger mkfastq command I need to specify --samplesheet or --csv file. according to the website of 10X genomics, the format of that file if we have multiple library types, looks like this:

Lane,Sample,Index
1,GEX_sample,SI-TT-D9
1,CMO_sample,SI-NN-A1

and I need to make a file almost like this since I also have multiple library types. but in our case, we have pulled the cells from different conditions and we want to have data from different conditions in a separate fastq file. once we demultiplexed the bcl files but we got all the reads from all samples in 2 fastq files (R1 and R2 which means like they are the same sample). how can I ask the program or make a new samplesheet or csv file, to have the reads from different conditions in separate fastq files?