#!/bin/sh

#if [ $# -ne 2 ]; then
#	echo "USAGE skeleton.sh InputFile OutputFile" 1>&2
#	exit 1
#fi


#$ -S /bin/sh # set shell in UGE

PATH="$HOME/temp/dstep/tools/bin:$PATH"; export PATH

#command
cellranger-atac count --id=emm_atac --reference=../data/refdata-cellranger-atac-mm10-1.2.0/ --fastqs=../../10X_ATAC_Lung/ --localcores=8 --localmem=90


#qsub -cwd -l s_vmem=2G,mem_req=2G ./cellranger.sh
#qsub -l s_vmem=12G -l mem_req=12G -pe def_slot 8 -cwd cellranger_atac.sh
