MiSeq 000000000-A9GDG demux

000000000-A9GDG.sh

#!/bin/bash

# load modules
module load bcl2fastq/gnu/1.8.4

CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/manual/140617_M02455_0020_000000000-A9GDG/Data/Intensities/BaseCalls/"
FASTQ_BASE="/scratch/gencore/manual"

SAMPLE_SHEET_HEAD="FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject"
BCL_TO_FASTQ_CMD="/share/apps/bcl2fastq/1.8.4/gnu/bin/configureBclToFastq.pl"
PBS_HEAD="
#!/bin/sh
#PBS -V
#PBS -l nodes=1:ppn=$CORES,walltime=48:00:00
#PBS -M $EMAIL
#PBS -m abe
#PBS -q s48
#PBS -l mem=16GB
module load ncurses/gnu/5.9
module load bcl2fastq/gnu/1.8.4
"
PBS_FOOT="
make -j$CORES
exit $?;
"

make_bcl2fastq_pbs() {
BCL_To_FASTQ_RUN=$1
echo -e "$PBS_HEAD
cd $FASTQ_BASE/$BCL_To_FASTQ_RUN/Unaligned
$PBS_FOOT$" > $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs
}

make_sample_sheet(){
BCL_To_FASTQ_RUN=$1
echo -e "$SAMPLE_SHEET_HEAD
$2" > $FASTQ_BASE/$BCL_To_FASTQ_RUN/SampleSheet.csv
}

# RUN
BCL_To_FASTQ_RUN="000000000-A9GDG"
mkdir -p "$FASTQ_BASE/$BCL_To_FASTQ_RUN"
make_bcl2fastq_pbs "$BCL_To_FASTQ_RUN"
make_sample_sheet $BCL_To_FASTQ_RUN "\
000000000-A9GDG,1,140618_GMS1,,GCCAAT,,N,,Gustavo Monteiro Silva,K63_ribosome_profiling
000000000-A9GDG,1,140618_GMS2,,CTTGTA,,N,,Gustavo Monteiro Silva,K63_ribosome_profiling
000000000-A9GDG,1,140618_GMS3,,TGACCA,,N,,Gustavo Monteiro Silva,K63_ribosome_profiling
000000000-A9GDG,1,140618_GMS4,,ACTTGA,,N,,Gustavo Monteiro Silva,K63_ribosome_profiling
"
echo -e "$BCL_TO_FASTQ_CMD --input-dir $BASECALLS  \
--output-dir $FASTQ_BASE/$BCL_To_FASTQ_RUN/Unaligned \
--sample-sheet $FASTQ_BASE/$BCL_To_FASTQ_RUN/SampleSheet.csv \
--fastq-cluster-count 0 \
--use-bases-mask \"Y51,I6\" \
--no-eamss \
--mismatches 1"
# qsub -N $BCL_To_FASTQ_RUN $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs