140617_SN911_0218_AC4G9YACXX Single index only

140617_SN911_0218_AC4G9YACXX.sh

#!/bin/bash

# load modules
# module unload bcl2fastq/gnu/1.8.4
# module load bcl2fastq/gnu/1.8.4

CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/hiseq-700911/140617_SN911_0218_AC4G9YACXX/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 unload bcl2fastq/gnu/1.8.4
# module load bcl2fastq/gnu/1.8.4
"

PBS_FOOT="
make -j$CORES
exit $?;
"

make_bcl2fastq_pbs() {
BCL_To_FASTQ_RUN=$1
CONFIG_BCL_To_FASTQ=$2

echo -e "$PBS_HEAD
$CONFIG_BCL_To_FASTQ

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
}

BCL_To_FASTQ_RUN="140617_SN911_0218_AC4G9YACXX"

mkdir -p "$FASTQ_BASE/$BCL_To_FASTQ_RUN"

make_sample_sheet $BCL_To_FASTQ_RUN "\
C4G9YACXX,2,1L22A,,ATCACG,,N,,Karen Hicks,moss
C4G9YACXX,2,3L22A,,CGATGT,,N,,Karen Hicks,moss
C4G9YACXX,2,13L22A,,TTAGGC,,N,,Karen Hicks,moss
C4G9YACXX,2,20L22A,,TGACCA,,N,,Karen Hicks,moss
C4G9YACXX,2,1L15A,,ACAGTG,,N,,Karen Hicks,moss
C4G9YACXX,2,3L15A,,GCCAAT,,N,,Karen Hicks,moss
C4G9YACXX,2,13L15A,,CAGATC,,N,,Karen Hicks,moss
C4G9YACXX,2,20L15A,,ACTTGA,,N,,Karen Hicks,moss
C4G9YACXX,2,1S15A,,GATCAG,,N,,Karen Hicks,moss
C4G9YACXX,2,3A15A,,TAGCTT,,N,,Karen Hicks,moss
C4G9YACXX,2,13S15A,,GGCTAC,,N,,Karen Hicks,moss
C4G9YACXX,2,20S15A,,CTTGTA,,N,,Karen Hicks,moss
C4G9YACXX,3,1L22B,,ATCACG,,N,,Karen Hicks,moss
C4G9YACXX,3,3L22B,,CGATGT,,N,,Karen Hicks,moss
C4G9YACXX,3,13L22B,,TTAGGC,,N,,Karen Hicks,moss
C4G9YACXX,3,20L22B,,TGACCA,,N,,Karen Hicks,moss
C4G9YACXX,3,1L15B,,ACAGTG,,N,,Karen Hicks,moss
C4G9YACXX,3,3L15B,,GCCAAT,,N,,Karen Hicks,moss
C4G9YACXX,3,13L15B,,CAGATC,,N,,Karen Hicks,moss
C4G9YACXX,3,20L15B,,ACTTGA,,N,,Karen Hicks,moss
C4G9YACXX,3,1S15B,,GATCAG,,N,,Karen Hicks,moss
C4G9YACXX,3,3A15B,,TAGCTT,,N,,Karen Hicks,moss
C4G9YACXX,3,13S15B,,GGCTAC,,N,,Karen Hicks,moss
C4G9YACXX,3,20S15B,,CTTGTA,,N,,Karen Hicks,moss
C4G9YACXX,4,1L22C,,ATCACG,,N,,Karen Hicks,moss
C4G9YACXX,4,3L22C,,CGATGT,,N,,Karen Hicks,moss
C4G9YACXX,4,13L22C,,TTAGGC,,N,,Karen Hicks,moss
C4G9YACXX,4,20L22C,,TGACCA,,N,,Karen Hicks,moss
C4G9YACXX,4,1L15C,,ACAGTG,,N,,Karen Hicks,moss
C4G9YACXX,4,3L15C,,GCCAAT,,N,,Karen Hicks,moss
C4G9YACXX,4,13L15C,,CAGATC,,N,,Karen Hicks,moss
C4G9YACXX,4,20L15C,,ACTTGA,,N,,Karen Hicks,moss
C4G9YACXX,4,1S15C,,GATCAG,,N,,Karen Hicks,moss
C4G9YACXX,4,3A15C,,TAGCTT,,N,,Karen Hicks,moss
C4G9YACXX,4,13S15C,,GGCTAC,,N,,Karen Hicks,moss
C4G9YACXX,4,20S15C,,CTTGTA,,N,,Karen Hicks,moss
C4G9YACXX,6,SDW_HiSeq_1,,CGATGT,,N,,Sally Warring,Tvag_RNASseq
C4G9YACXX,6,SDW_HiSeq_2,,TGACCA,,N,,Sally Warring,Tvag_RNASseq
C4G9YACXX,6,SDW_HiSeq_3,,ACAGTG,,N,,Sally Warring,Tvag_RNASseq
C4G9YACXX,6,SDW_HiSeq_4,,GCCAAT,,N,,Sally Warring,Tvag_RNASseq
C4G9YACXX,6,SDW_HiSeq_5,,CTTGTA,,N,,Sally Warring,Tvag_RNASseq
C4G9YACXX,6,SDW_HiSeq_6,,GTGAAA,,N,,Sally Warring,Tvag_RNASseq
C4G9YACXX,7,ZL1,,CGATGT,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL2,,TGACCA,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL3,,ACAGTG,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL4,,GCCAAT,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL5,,CAGATC,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL6,,CTTGTA,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL7,,ATCACG,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,7,ZL8,,TTAGGC,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL1,,CGATGT,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL2,,TGACCA,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL3,,ACAGTG,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL4,,GCCAAT,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL5,,CAGATC,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL6,,CTTGTA,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL7,,ATCACG,,N,,Zunping Luo,Hybrid_Selection
C4G9YACXX,8,ZL8,,TTAGGC,,N,,Zunping Luo,Hybrid_Selection
"

make_bcl2fastq_pbs "$BCL_To_FASTQ_RUN" "$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*,I6nn,n*,n*\" \
--tiles \"s_2,s_3,s_4,s_6,s_7,s_8\" \
--no-eamss \
--mismatches 1"

qsub -N $BCL_To_FASTQ_RUN $FASTQ_BASE/$BCL_To_FASTQ_RUN/bcl2fastq.pbs