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Copy pathCreate_Makeflow.sh
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Create_Makeflow.sh
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INpath=$1
SID=$2
Module=$3
Lanemkflow()
{
INp=$1
OUp=$2
cat $INp >> $OUp
cat>>$OUp<<EOF
CATEGORY="fastqclink.${AID}"
CORES=7
MEMORY=30000
DISK=10
${RawFQpre}_r1.fq.gz ${RawFQpre}_r2.fq.gz : ${R1} ${R2}
sh $WORKFLOW_DIR/FastqLink $INp
CATEGORY="cutadapt.trim.${AID}"
CORES=12
MEMORY=30000
DISK=10
${CUTADAPTpre}_trimmed_1.fq.gz ${CUTADAPTpre}_trimmed_2.fq.gz : ${RawFQpre}_r1.fq.gz ${RawFQpre}_r2.fq.gz
sh $WORKFLOW_DIR/CUTAdapt $INp
CATEGORY="fastqc.${AID}"
CORES=7
MEMORY=30000
DISK=10
${FASTQCpre}_r1_fastqc.html ${FASTQCpre}_trimmed_2_fastqc.html : ${RawFQpre}_r1.fq.gz ${RawFQpre}_r2.fq.gz ${CUTADAPTpre}_trimmed_1.fq.gz ${CUTADAPTpre}_trimmed_2.fq.gz
sh $WORKFLOW_DIR/FastQC $INp
CATEGORY="trim_galore.${AID}"
CORES=7
MEMORY=30000
DISK=10
${TRIMGALpre}_val_1.fq.gz ${TRIMGALpre}_val_2.fq.gz : ${RawFQpre}_r1.fq.gz ${RawFQpre}_r2.fq.gz
sh $WORKFLOW_DIR/TRIMGalore $INp
CATEGORY="bwa_mem.${AID}"
CORES=7
MEMORY=20000
DISK=10
${BAMout}/${AID}.bam : ${CUTADAPTpre}_trimmed_1.fq.gz ${CUTADAPTpre}_trimmed_2.fq.gz
sh $WORKFLOW_DIR/BWAmem $INp ${CUTADAPTpre}_trimmed_1.fq.gz ${CUTADAPTpre}_trimmed_2.fq.gz
EOF
}
Repmkflow()
{
INp=$1
OUp=$2
cat $INp >> $OUp
cat>>$OUp<<EOF
CATEGORY="bwa.trans.${TID}"
CORES=7
MEMORY=20000
DISK=10
$BAMmkdup : ${BAMreplane[@]}
sh $WORKFLOW_DIR/BAMtrans $INp
CATEGORY="bam.filter.${TID}"
CORES=7
MEMORY=20000
DISK=10
$BAMfilter ${BAMfilter}.bai : $BAMmkdup
sh $WORKFLOW_DIR/BAMfilter $INp $BAMmkdup
CATEGORY="bam.stat.${TID}"
CORES=7
MEMORY=20000
DISK=10
$BAMstatout : $BAMmkdup
sh $WORKFLOW_DIR/BAMstat $INp $BAMmkdup
CATEGORY="bam.deepstat.${TID}"
CORES=7
MEMORY=20000
DISK=10
${DEEPTpre}.heatmap.gz ${DEEPTpre}.Heatmap1sortedRegions.bed : $BAMfilter
sh $WORKFLOW_DIR/DEEPTstate $INp $BAMfilter
${BIGWIGpre}.scaled.bigWig : $BAMfilter
sh $WORKFLOW_DIR/BIGWIG $INp $BAMfilter
CATEGORY="callpeak.macs2.${TID}"
CORES=7
MEMORY=20000
DISK=10
${MACS2cppre}_peaks.narrowPeak ${MACS2cppre}_summits.bed : $BAMfilter
sh $WORKFLOW_DIR/MACS2_CallPeak $INp $BAMfilter
${MACS2cppre}_peaks.narrowPeak.fCounts.txt : ${MACS2cppre}_peaks.narrowPeak $BAMfilter
sh $WORKFLOW_DIR/FRIP $INp ${MACS2cppre}_peaks.narrowPeak $BAMfilter
CATEGORY="callpeak.genrich.${TID}"
CORES=7
MEMORY=20000
DISK=10
${GENRICHpre}_genrich.peaks.narrowPeak : $BAMfilter
sh $WORKFLOW_DIR/GENRICH_CallPeak $INp $BAMfilter
${GENRICHpre}_genrich.peaks.narrowPeak.fCounts.txt : ${GENRICHpre}_genrich.peaks.narrowPeak $BAMfilter
sh $WORKFLOW_DIR/FRIP $INp ${GENRICHpre}_genrich.peaks.narrowPeak $BAMfilter
CATEGORY="callpeak.annotate.homer.${TID}"
CORES=7
MEMORY=20000
DISK=10
${HOMERpre}_peaks.annotatePeaks.txt : ${MACS2cppre}_peaks.narrowPeak
sh $WORKFLOW_DIR/HOMER_Anno $INp ${MACS2cppre}_peaks.narrowPeak
${HOMERpre}/homerResults.html : ${MACS2cppre}_peaks.narrowPeak
sh $WORKFLOW_DIR/HOMER_Motifs $INp ${MACS2cppre}_peaks.narrowPeak
CATEGORY="ataqv.qc.${TID}"
CORES=7
MEMORY=20000
DISK=10
${ATAQCpre}.ataqv.json.gz : $BAMfilter ${MACS2cppre}_peaks.narrowPeak
sh $WORKFLOW_DIR/ATAQV $INp $BAMfilter ${MACS2cppre}_peaks.narrowPeak
$ATAQCout/$SID/index.html : ${ATAQCrep[@]}
sh $WORKFLOW_DIR/MKARV $INp
${IDRpre}.idrValues.txt : ${IDRPeak[@]}
sh $WORKFLOW_DIR/IDR $INp
EOF
}
INSf=( $INpath/${SID}__D*${Module}.input )
. ${INSf[0]}
WorkSH=$AUT/WorkShell
SampMK=$WorkSH/${SID}_${Module}.mf
if [ -f $SampMK ];then
rm $SampMK
fi
mkdir -p $WorkSH
#########each lane
for i in ${INSf[@]};do
. $i
. $WORKFLOW_DIR/env.Variable
cp $i $WorkSH/${AID}_${Module}.input
Lanemkflow $WorkSH/${AID}_${Module}.input $SampMK
done
#########each rep
for j in ${TIDs[@]};do
Tidf=( $WorkSH/${j}*${Module}.input )
. ${Tidf[0]}
. $WORKFLOW_DIR/env.Variable
Repmkflow ${Tidf[0]} $SampMK
done