140703_M02455_0021_000000000-A8P38 demux

140703_M02455_0021_000000000-A8P38.sh

#!/bin/bash
 
# load modules
# module load bcl2fastq/gnu/1.8.4
 
CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/manual/140703_M02455_0021_000000000-A8P38/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 $EMAIL
#PBS -m abe
#PBS -q s48
#PBS -l mem=16GB
module load bcl2fastq/gnu/1.8.4
"
PBS_FOOT="
make -j$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-A8P38"
mkdir -p "$FASTQ_BASE/$BCL_To_FASTQ_RUN"
make_bcl2fastq_pbs "$BCL_To_FASTQ_RUN"
make_sample_sheet $BCL_To_FASTQ_RUN "\
000000000-A8P38,1,Undetermined,,Undetermined,,N,,Pui Ling,A8P38
000000000-A8P38,1,MPa,,CGATGT,,N,,Pui Ling,A8P38
000000000-A8P38,1,MPb,,TGACCA,,N,,Pui Ling,A8P38
000000000-A8P38,1,MPc,,ACAGTG,,N,,Pui Ling,A8P38
000000000-A8P38,1,MP2,,GCCAAT,,N,,Pui Ling,A8P38
000000000-A8P38,1,MP3,,CAGATC,,N,,Pui Ling,A8P38
000000000-A8P38,1,MP5,,CTTGTA,,N,,Pui Ling,A8P38
000000000-A8P38,1,MP6,,AGTCAA,,N,,Pui Ling,A8P38
000000000-A8P38,1,MP7,,AGTTCC,,N,,Pui Ling,A8P38
000000000-A8P38,1,MP8,,ATGTCA,,N,,Pui Ling,A8P38
000000000-A8P38,1,MPuncut2,,CCGTCC,,N,,Pui Ling,A8P38
000000000-A8P38,1,MPuncut3,,GTCCGC,,N,,Pui Ling,A8P38
000000000-A8P38,1,MPuncut6,,GTGAAA,,N,,Pui Ling,A8P38
"
echo -e "$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 \"Y*,I*\" \
--no-eamss \
--mismatches 1"|bash
qsub -N $BCL_To_FASTQ_RUN $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs