added qc flag (1646cb49) · Commits · Chaos / chaos.juicer

SLURM/scripts/juicer.sh

+24 −2

Changes for SLURM/scripts/juicer.sh: 24 added lines, 2 removed lines.
Original line number	Diff line number	Diff line
		@@ -174,7 +174,7 @@ sampleName="HiC_sample"
		libraryName="HiC_library"

		## Read arguments
		usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-q queue] [-l long queue] [-s site]\n [-a about] [-S stage] [-p chrom.sizes path] [-C chunk size]\n [-y restriction site file] [-z reference genome file]\n [-D Juicer scripts parent dir] [-Q queue time limit]\n [-L long queue time limit] [-b ligation] [-t threads]\n [-T threadsHic] [-A account] [-i sample] [-k library] [-w wobble]\n [-e] [-h] [-f] [-j] [-u] [--assembly] [--cleanup] [--qc_apa]"
		usageHelp="Usage: ${0##*/} [-g genomeID] [-d topDir] [-q queue] [-l long queue] [-s site]\n [-a about] [-S stage] [-p chrom.sizes path] [-C chunk size]\n [-y restriction site file] [-z reference genome file]\n [-D Juicer scripts parent dir] [-Q queue time limit]\n [-L long queue time limit] [-b ligation] [-t threads]\n [-T threadsHic] [-A account] [-i sample] [-k library] [-w wobble]\n [-e] [-h] [-f] [-j] [-u] [--assembly] [--cleanup] [--qc_apa] [--qc]"
		genomeHelp="* [genomeID] must be defined in the script, e.g. \"hg19\" or \"mm10\" (default \n \"$genomeID\"); alternatively, it can be defined using the -z command"
		dirHelp="* [topDir] is the top level directory (default\n \"$topDir\")\n [topDir]/fastq must contain the fastq files\n [topDir]/splits will be created to contain the temporary split files\n [topDir]/aligned will be created for the final alignment"
		queueHelp="* [queue] is the queue for running alignments (default \"$queue\")"
		@@ -203,6 +203,7 @@ singleEndHelp="* -u: Single end alignment"
		assemblyHelp="* --assembly: For use before 3D-DNA; early exit and create old style merged_nodups"
		cleanupHelp="* --cleanup: Automatically clean up files if pipeline successfully completes"
		qcapaHelp="* --qc_apa: Run QC APA"
		qcHelp="* --qc: Only build map down to 1000bp"
		helpHelp="* -h, --help: print this help and exit"

		printHelpAndExit() {
		@@ -235,6 +236,7 @@ printHelpAndExit() {
		echo -e "$assemblyHelp"
		echo -e "$cleanupHelp"
		echo -e "$qcapaHelp"
		echo -e "$qcHelp"
		echo "$helpHelp"
		exit "$1"
		}
		@@ -271,6 +273,7 @@ while getopts "d:g:a:hq:s:p:l:y:z:S:C:D:Q:L:b:A:i:t:jfuec-:T:w:k:" opt; do
		assembly) earlyexit=1; assembly=1 ;;
		cleanup) cleanup=1 ;;
		qc_apa) qc_apa=1 ;;
		qc) qc=1 ;;
		"help") printHelpAndExit 0;;
		*) echo "Unknown argument --${OPTARG}";
		printHelpAndExit 1;;
		@@ -1389,13 +1392,22 @@ FINCLN1`
		time ${juiceDir}/scripts/index_by_chr.awk ${outputdir}/merged1.txt 500000 > ${outputdir}/merged1_index.txt
		fi


		if [ "$qc" -eq 1 ]
		then
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		fi
		else
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter.txt -g $outputdir/inter_hists.m -q 1 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHicString $outputdir/merged1.txt $outputdir/inter.hic $genomePath
		fi
		fi
		time ${juiceDir}/scripts/juicer_tools addNorm $threadNormString ${outputdir}/inter.hic
		rm -Rf ${outputdir}"/HIC_tmp"
		date
		@@ -1432,12 +1444,22 @@ HIC`
		time ${juiceDir}/scripts/index_by_chr.awk ${outputdir}/merged30.txt 500000 > ${outputdir}/merged30_index.txt
		fi

		if [ "$qc" -eq 1 ]
		then
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		fi
		else
		if [ "$nofrag" -eq 1 ]
		then
		time ${juiceDir}/scripts/juicer_tools pre -n -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		else
		time ${juiceDir}/scripts/juicer_tools pre -n -f $site_file -s $outputdir/inter_30.txt -g $outputdir/inter_30_hists.m -q 30 -r 2500000,1000000,500000,250000,100000,50000,25000,10000,5000,2000,1000,500,200,100 $threadHic30String $outputdir/merged30.txt $outputdir/inter_30.hic $genomePath
		fi
		fi
		time ${juiceDir}/scripts/juicer_tools addNorm $threadNormString ${outputdir}/inter_30.hic
		rm -Rf ${outputdir}"/HIC30_tmp"
		date

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