sge_2_spaceranger.batch

#!/bin/bash

#$ -S /bin/bash
#$ -pe smp 4
#$ -l tmem=80G
#$ -l h_vmem=80G
#$ -l h_rt=24:00:00
#$ -N spaceranger
#$ -cwd

export PATH=/share/apps/genomics/bcl2fastq2-2.20/bin:$PATH
export PATH=/share/apps/genomics/spaceranger-2.0.0/bin:$PATH


slide=$(cat ${SGE_O_WORKDIR}/spaceranger_inputs/${sample}_config.csv | sed 's/\./\t/g' | awk '{print $1}')
area=$(cat ${SGE_O_WORKDIR}/spaceranger_inputs/${sample}_config.csv | sed 's/\./\t/g' | awk '{print $2}')


echo ${JOB_NAME} "for "${sample}
echo "=========="
echo ""
echo "Job "${JOB_ID} "starts "$(date)" on "$(hostname)
echo ""
##########


mkdir ${SGE_O_WORKDIR}/results_spaceranger/${sample}
cd ${SGE_O_WORKDIR}/results_spaceranger/${sample}


echo "#####"
echo "Starting 10X Space Ranger Pipeline"
echo "#####"


NO_OF_CORES=4
MEMORY_REQUIRED=72


#spaceranger count --localcores ${NO_OF_CORES} --localmem ${MEMORY_REQUIRED} --id ${sample} --transcriptome /SAN/colcc/cellranger_references/refdata-gex-GRCh38-2020-A --fastqs ${SGE_O_WORKDIR}/RAW/${sample}/. --image ${SGE_O_WORKDIR}/spaceranger_inputs/${sample}_tissue_image.tif --slide $slide --area $area --probe-set ${SGE_O_WORKDIR}/spaceranger_inputs/${sample}_probe_set.csv --sample ${sample}_1,${sample}_2

spaceranger count --localcores ${NO_OF_CORES} --localmem ${MEMORY_REQUIRED} --id ${sample} --transcriptome /SAN/colcc/cellranger_references/refdata-gex-GRCh38-2020-A --fastqs ${SGE_O_WORKDIR}/RAW/${sample}/. --cytaimage ${SGE_O_WORKDIR}/spaceranger_inputs/${sample}_CytAssist_image.tif --slide $slide --area $area --probe-set ${SGE_O_WORKDIR}/spaceranger_inputs/${sample}_probe_set.csv --sample ${sample}_1,${sample}_2




##########
echo ""
echo "Job "${JOB_ID} "ends "$(date)