batch run for cellranger count
perl batchCellrangerCounter.pl --help
version 1.0, October 2018
usage: batchCellrangerCounter.pl
-f|--fastq
path to FastQ files (required)
-o|--output-dir
path to output directory (required)
-g|--genome
path to genome index (required)
-p|--opts
additional Cellranger Count parameters
-h|--help
print help message
-v|--version
print current version
example:
perl batchCellrangerCounter.pl --fastq /path/to/fastq/ --output-dir /path/to/projec/cellranger_count_out/ --genome /path/to/genome/alien/cellranger/ --opts "--chemistry SC3Pv2 --localcores=32 --force-cells=7000"