Demultiplex 140430_SN7001341_0074_AC49ANACXX

140430_SN7001341_0074_AC49ANACXX.sh

#!/bin/bash

CORES=8
BASECALLS="/share/140430_SN7001341_0074_AC49ANACXX/Data/Intensities/BaseCalls/"
FASTQ_BASE="/share/manual"

SAMPLE_SHEET_HEAD="FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject"
BCL_TO_FASTQ_CMD="/usr/local/bin/configureBclToFastq.pl"

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="C49ANACXX"
mkdir -p "$FASTQ_BASE/$BCL_To_FASTQ_RUN"
make_sample_sheet $BCL_To_FASTQ_RUN "\
C49ANACXX,1,503,,Undetermined,,N,,,Lane1
C49ANACXX,2,UndeterminedLane2,,Undetermined,,N,,,Lane2
C49ANACXX,2,3112,,TGACCA,,N,,,Lane2
C49ANACXX,2,3222,,ACAGTG,,N,,,Lane2
C49ANACXX,3,UndeterminedLane3,,Undetermined,,N,,,Lane3
C49ANACXX,3,WS-3,,GCCAAT,,N,,,Lane3
C49ANACXX,3,WS-7,,CAGATC,,N,,,Lane3
C49ANACXX,4,PhiX_v3,,Undetermined,,N,,,Lane4
C49ANACXX,5,RSSF,,Undetermined,,N,,,Lane5
C49ANACXX,6,M2,,Undetermined,,N,,,Lane6
C49ANACXX,7,CF,,Undetermined,,N,,,Lane7
C49ANACXX,8,X1,,Undetermined,,N,,,Lane8
"
echo -e "$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 \
--no-eamss \
--mismatches 1"|bash
echo "cd $FASTQ_BASE/$BCL_To_FASTQ_RUN/Unaligned && make -j$CORES"|bash