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modified: bcl2fastq.sh
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naumenko-sa committed Jul 11, 2017
1 parent 74ba0b9 commit c3b2ae9
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4 changes: 3 additions & 1 deletion bcl2fastq.sh
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#PBS -l walltime=23:00:00,nodes=1:ppn=10
#PBS -joe .
#PBS -d .
#PBS -l vmem=20g,mem=20g
#PBS -l vmem=30g,mem=30g

if [ -z $sample_sheet ];
then
sample_sheet=$1
fi

#2.19 needs 20G of RAM for 10 threads
# sometimes 20G is not enough - I've got an error
# bcl2fastq is designed up to 32G
module load bcl2fastq

#I use no-lane splitting, and the result fastq files could not be uploaded to basespace
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