/oak/stanford/groups/akundaje/marinovg/programs/bcl2fastq2-v2.20/export/bin/bcl2fastq -p 8 --mask-short-adapter-reads 0 --barcode-mismatches 1 --ignore-missing-filter --min-log-level WARNING --minimum-trimmed-read-length 75 --runfolder-dir /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-03-25-NextSeq-run/180325_NS500418_0814_AHKWVJBGX5 --output-dir /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-03-25-NextSeq-run --stats-dir /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-03-25-NextSeq-run/bcl2fastq-stats --reports-dir /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2018-03-25-NextSeq-run/bcl2fastq-reports --sample-sheet SampleSheet.csv