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fwip/run_bcl2fastq.sh

Last active August 29, 2015 14:17
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run_bcl2fastq.sh
qsub -cwd -N "u-H3MHT" -pe threads 8 -V -S /bin/bash <<'__FASTQ__'
set -x -e -o pipefail
cd "/net/glados/solexa_data/150109_NS500372_0058_AH3MHTBGXX"
bcl2fastq \
--input-dir "/net/glados/solexa_data/150109_NS500372_0058_AH3MHTBGXX/Data/Intensities/BaseCalls" \
--use-bases-mask "y36,I6n,y36" \
--output-dir "/net/glados/solexa_data/150109_NS500372_0058_AH3MHTBGXX/fastq" \
--with-failed-reads \
--barcode-mismatches "0" \
--loading-threads $(( NSLOTS / 4 + 1 )) \
--writing-threads $(( NSLOTS / 4 + 1 )) \
--demultiplexing-threads $(( NSLOTS / 2 + 1 )) \
--processing-threads $(( NSLOTS / 3 + 1 ))
__FASTQ__
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