#!/bin/sh # Grid Engine options (lines prefixed with #$) #$ -N arrayRunCellRangerCombined_human # job name #$ -cwd #$ -l h_rt=30:00:00 #$ -l h_vmem=12G #$ -pe sharedmem 16 #$ -M YourEmailAdress #$ -m beas #$ -P scs_speedup # Initialise the environment modules . /etc/profile.d/modules.sh module load igmm/apps/cellranger/6.0.2 # check if this is the Cellranger version you would like to use. # versions available in Eddie can be seen with the command `module available` #$ -t 1-9 #ID file IDFILE=/exports/eddie/scratch/$USER/Chimeras/Data/all-samples-except-ddh20A.txt # Assigning SAMPLE variable from the built-in array counter SAMPLE=`sed -n ${SGE_TASK_ID}p "$IDFILE"` # Variables # Acess the temporary access to the physical disk on the node where the job runs. cd $TMPDIR # You can change the SAMPLE variable name or submit the script as: runCellranger.sh <sample name> # ex: runCellranger.sh 11723WAPool02-S__12_25_17_CB # SAMPLE="11723WAPool02-S__12_25_17_CB" #SAMPLE=$1 # Path to the Reference Genome directory REFGENOME="/exports/eddie/scratch/$USER/refdata-gex-GRCh38-2020-A" # Path to the directory where the samples are FASTQS="/exports/eddie/scratch/$USER/Chimeras/Data/Raw_Data/$SAMPLE*" # Create a proper directory for the fastq files mkdir -p ${SAMPLE}_fastqs cp $FASTQS ${SAMPLE}_fastqs #Running echo run cellranger count --id="$SAMPLE" --transcriptome="$REFGENOME" --fastqs="${SAMPLE}_fastqs" cellranger count --id="$SAMPLE" \ --transcriptome="$REFGENOME" \ --fastqs="${SAMPLE}_fastqs" mkdir -p /exports/eddie/scratch/s1241040/Chimeras/outs/filter_70/CellRanger-combined/human rsync -rl $SAMPLE /exports/eddie/scratch/s1241040/Chimeras/outs/filter_70/CellRanger-combined/human