#!/bin/sh
# Grid Engine options (lines prefixed with #$)
#$ -N run-cellranger # job name
#$ -cwd
#$ -l h_rt=30:00:00
#$ -l h_vmem=12G
#$ -pe sharedmem 16 
#$ -M YourEmailAdress   
#$ -m beas 
# 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 1-10

#ID file
IDFILE=/exports/eddie/scratch/$USER/Chimeras/Data/samples.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/$USER/Chimeras/Data/SplitSpecies/human/Method1/fastqs/$SAMPLE"


#Running
echo run cellranger count --id="$SAMPLE" --transcriptome="$REFGENOME" --fastqs="$FASTQS" 

cellranger count --id="$SAMPLE" \
                   --transcriptome="$REFGENOME" \
                   --fastqs="$FASTQS" 

mkdir -p /exports/cmvm/eddie/scs/groups/Williamsdata/Chimeras/outs/filter_70/CellRanger-onlyCB-uniq-reads/human
rsync -rl $SAMPLE /exports/cmvm/eddie/scs/groups/Williamsdata/Chimeras/outs/filter_70/CellRanger-onlyCB-uniq-reads/human