Merge pull request #195 from gringer/yaml-noedit (991165d5) · Commits · github_fork / ZUMIs

checkyaml.R

+37 −32

Original line number	Original line	Diff line number	Diff line
	#!/usr/bin/env Rscript		#!/usr/bin/env Rscript

	suppressMessages(require(yaml))		suppressMessages(
			if(!require(yaml)){
			stop("Library 'yaml' is needed by R; please install it");
			})
	y<-commandArgs(trailingOnly = T)		y<-commandArgs(trailingOnly = T)

	inp<-try(read_yaml(y),silent = T)		inp<-try(read_yaml(y),silent = T)
	@@ -10,7 +13,7 @@ e=0
	if(grepl("try-error",class(inp))) {		if(grepl("try-error",class(inp))) {
	e=1		e=1
	print(e)		print(e)
	stop()		stop("Syntax error loading yaml file")
	}		}


	@@ -60,7 +63,8 @@ print(
	function(x) {		function(x) {
	if(is.null(unlist(inp$sequence_files[[x]]$name))) {		if(is.null(unlist(inp$sequence_files[[x]]$name))) {
	e=1		e=1
	print(paste(print(names(inp$sequence_files[x])),": You need to provide path to the input file"))		print(paste(print(names(inp$sequence_files[x])),
			": You need to provide a path for this input file"))
	}else{ print("")}		}else{ print("")}
	})		})
	))		))
	@@ -70,7 +74,8 @@ print(
	function(x) {		function(x) {
	if(is.null(unlist(inp$sequence_files[[x]]$base_definition))) {		if(is.null(unlist(inp$sequence_files[[x]]$base_definition))) {
	e=1		e=1
	print(paste(print(names(inp$sequence_files[x])),": You need to provide base definitions for this input file"))}		print(paste(print(names(inp$sequence_files[x])),
			": You need to provide base definitions for this input file"))}
	})		})
	)		)
	)		)
	@@ -80,7 +85,7 @@ lapply(inp$sequence_files,
	if(!is.null(x$base_definition)) {		if(!is.null(x$base_definition)) {
	if(any(!grepl("^BC\|^UMI\|^cDNA",x$base_definition))) {		if(any(!grepl("^BC\|^UMI\|^cDNA",x$base_definition))) {
	e=1		e=1
	print("The base definition can only be BC/cDNA/UMI. Check if you have a typo/special characters in your base definition or you forgot to add /space/ after -. Refer to the example yaml.")		print("The base definition can only be BC/cDNA/UMI. Check if you have a typo/special characters in your base definition or you forgot to add /space/ after -. Refer to the example yaml in the zUMIs installation directory.")
	}		}
	}		}
	})		})

zUMIs-master.sh

+172 −173

Original line number	Original line	Diff line number	Diff line
	@@ -4,16 +4,18 @@
	# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann		# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
	# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se		# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se
	vers=2.8.3		vers=2.8.3
	currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh \| grep '^vers=' \| cut -f2 -d "="`		currentv=$(curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh \| grep '^vers=' \| cut -f2 -d "=")
	if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi		if [ "$currentv" != "$vers" ] ; then
			echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------";
			fi

	function check_opts() {		function check_opts() {
	value=$1		value=$1
	name=$2		name=$2
	flag=$3		flag=$3

	if [[ -z "$value" ]]		if [[ -z "${value}" ]] ; then
	then failure "No $name!! One can not run this pipeline without $flag option."		failure "No ${name}!! One can not run this pipeline without ${flag} option."
	fi		fi
	}		}

	@@ -28,7 +30,7 @@ zumis=$0
	function usage () {		function usage () {
	cat >&2 <<EOF		cat >&2 <<EOF

	USAGE: $zumis [options]		USAGE: ${zumis} [options]
	-h Print the usage info.		-h Print the usage info.

	## Required parameters ##		## Required parameters ##
	@@ -42,238 +44,239 @@ function usage () {

	-c : Use zUMIs dependencies in the preinstalled conda enviroment.		-c : Use zUMIs dependencies in the preinstalled conda enviroment.

	zUMIs version $vers		zUMIs version ${vers}

	EOF		EOF
	}		}

	# Define the default variables #		# Define the default variables #
	zumisdir=$(dirname `readlink -f $0`)		zumisdir=$(dirname $(readlink -f $0))


	while getopts ":y:d:ch" options; do #Putting <:> between keys implies that they can not be called without an argument.		while getopts ":y:d:ch" options; do #Putting <:> between keys implies that they can not be called without an argument.
	case $options in		case ${options} in
	y ) yaml=$OPTARG;;		y ) yaml=${OPTARG};;
	d ) zumisdir=$OPTARG;;		d ) zumisdir=${OPTARG};;
	c ) conda=true;;		c ) conda=true;;
	h ) usage		h ) usage
	exit 1;;		exit 1;;
	\? ) echo -e "\n This key is not available! Please check the usage again: -$OPTARG"		\? ) echo -e "\n This key is not available! Please check the usage again: -${OPTARG}"
	usage		usage
	exit 1;;		exit 1;;
	esac		esac
	done		done

	if [[ $OPTIND -eq 1 ]] ; then		if [[ ${OPTIND} -eq 1 ]] ; then
	usage		usage
	exit 1		exit 1
	fi		fi

	check_opts "$yaml" "YAML" "-y"		check_opts "${yaml}" "YAML" "-y"

			# create temporary YAML file for corrected options
			yaml_orig=${yaml}
			yaml=$(dirname ${yaml})/$(basename ${yaml} .yaml).corrected.yaml
			cp ${yaml_orig} ${yaml}

	#now get some variables from YAML		#now get some variables from YAML
	num_threads=`grep 'num_threads' $yaml \| awk '{print $2}'`		num_threads=$(grep 'num_threads' ${yaml} \| awk '{print $2}')
	project=`grep 'project:' $yaml \| awk '{print $2}'`		project=$(grep 'project:' ${yaml} \| awk '{print $2}')
	whichStage=`grep 'which_Stage:' $yaml \| awk '{print $2}'`		whichStage=$(grep 'which_Stage:' ${yaml} \| awk '{print $2}')
	outdir=`grep 'out_dir' $yaml \| awk '{print $2}'`		outdir=$(grep 'out_dir' ${yaml} \| awk '{print $2}')
	genomedir=`grep 'STAR_index:' $yaml \| awk '{print $2}'`		genomedir=$(grep 'STAR_index:' ${yaml} \| awk '{print $2}')
	mem_limit=`grep 'mem_limit:' $yaml \| awk '{print $2}'`		mem_limit=$(grep 'mem_limit:' ${yaml} \| awk '{print $2}')
	isstats=`grep 'make_stats:' $yaml \| awk '{print $2}'`		isstats=$(grep 'make_stats:' ${yaml} \| awk '{print $2}')
	fqfiles=`grep 'name:' $yaml \| awk '{print $2}'`		fqfiles=$(grep 'name:' ${yaml} \| awk '{print $2}')
	velo=`grep 'velocyto:' $yaml \| awk '{print $2}'`		velo=$(grep 'velocyto:' ${yaml} \| awk '{print $2}')
	staridxdir=`grep 'STAR_index:' $yaml \| awk '{print $2}'`		staridxdir=$(grep 'STAR_index:' ${yaml} \| awk '{print $2}')


	if grep -q 'samtools_exec:' $yaml		if grep -q 'samtools_exec:' ${yaml} ; then
	then		samtoolsexc=$(grep 'samtools_exec' ${yaml} \| awk '{print $2}')
	samtoolsexc=`grep 'samtools_exec' $yaml \| awk '{print $2}'`
	else		else
	samtoolsexc=samtools		samtoolsexc=samtools
	echo "samtools_exec: $samtoolsexc" >> $yaml		echo "samtools_exec: ${samtoolsexc}" >> ${yaml}
	fi		fi

	if grep -q 'pigz_exec:' $yaml		if grep -q 'pigz_exec:' ${yaml} ; then
	then		pigzexc=$(grep 'pigz_exec' ${yaml} \| awk '{print $2}')
	pigzexc=`grep 'pigz_exec' $yaml \| awk '{print $2}'`
	else		else
			echo "Warning: YAML file doesn't include 'pigz_exec' option; setting to 'pigz'"
	pigzexc=pigz		pigzexc=pigz
	echo "pigz_exec: $pigzexc" >> $yaml		echo "pigz_exec: ${pigzexc}" >> ${yaml}
	fi		fi

	if grep -q 'STAR_exec:' $yaml		if grep -q 'STAR_exec:' ${yaml} ; then
	then		starexc=$(grep 'STAR_exec' ${yaml} \| awk '{print $2}')
	starexc=`grep 'STAR_exec' $yaml \| awk '{print $2}'`
	else		else
			echo "Warning: YAML file doesn't include 'STAR_exec' option; setting to 'STAR'"
	starexc=STAR		starexc=STAR
	echo "STAR_exec: $starexc" >> $yaml		echo "STAR_exec: ${starexc}" >> ${yaml}
	fi		fi

	if grep -q 'Rscript_exec:' $yaml		if grep -q 'Rscript_exec:' ${yaml} ; then
	then		Rexc=$(grep 'Rscript_exec' ${yaml} \| awk '{print $2}')
	Rexc=`grep 'Rscript_exec' $yaml \| awk '{print $2}'`
	else		else
			echo "Warning: YAML file doesn't include 'Rscript_exec' option; setting to 'Rscript'"
	Rexc=Rscript		Rexc=Rscript
	echo "Rscript_exec: $Rexc" >> $yaml		echo "Rscript_exec: ${Rexc}" >> ${yaml}
	fi		fi

	#check for conda usage!		#check for conda usage!
	if [[ $conda = true ]]; then		if [[ ${conda} = true ]] ; then
	echo "Using miniconda environment for zUMIs!"		echo "Using miniconda environment for zUMIs!"
			echo " note: internal executables will be used instead of those specified in the YAML file!"
	samtoolsexc=samtools		samtoolsexc=samtools
	if grep -q 'samtools_exec:' $yaml; then		if grep -q 'samtools_exec:' ${yaml} ; then
	sed -i '/samtools_exec:/d' $yaml		sed -i '/samtools_exec:/d' ${yaml}
	fi		fi
	echo "samtools_exec: $samtoolsexc" >> $yaml		echo "samtools_exec: ${samtoolsexc}" >> ${yaml}
	pigzexc=pigz		pigzexc=pigz
	if grep -q 'pigz_exec:' $yaml; then		if grep -q 'pigz_exec:' ${yaml} ; then
	sed -i '/pigz_exec:/d' $yaml		sed -i '/pigz_exec:/d' ${yaml}
	fi		fi
	echo "pigz_exec: $pigzexc" >> $yaml		echo "pigz_exec: ${pigzexc}" >> ${yaml}
	starexc=STAR		starexc=STAR
	if grep -q 'STAR_exec:' $yaml; then		if grep -q 'STAR_exec:' ${yaml} ; then
	sed -i '/STAR_exec:/d' $yaml		sed -i '/STAR_exec:/d' ${yaml}
	fi		fi
	echo "STAR_exec: $starexc" >> $yaml		echo "STAR_exec: ${starexc}" >> ${yaml}
	Rexc=Rscript		Rexc=Rscript
	if grep -q 'Rscript_exec:' $yaml; then		if grep -q 'Rscript_exec:' ${yaml} ; then
	sed -i '/Rscript_exec:/d' $yaml		sed -i '/Rscript_exec:/d' ${yaml}
	fi		fi
	echo "Rscript_exec: $Rexc" >> $yaml		echo "Rscript_exec: ${Rexc}" >> ${yaml}

	zumisenv=$zumisdir/zUMIs-env		zumisenv=${zumisdir}/zUMIs-env
	miniconda=$zumisdir/zUMIs-miniconda.tar.bz2		miniconda=${zumisdir}/zUMIs-miniconda.tar.bz2
	#check if zUMIs environment has been unpacked from tar		#check if zUMIs environment has been unpacked from tar
	if [[ ! -d $zumisenv ]] \|\| [[ $zumisdir/zUMIs-miniconda.partaa -nt $zumisenv ]] ; then		if [[ ! -d ${zumisenv} ]] \|\| [[ ${zumisdir}/zUMIs-miniconda.partaa -nt ${zumisenv} ]] ; then
	[ -d $zumisenv ] \|\| mkdir -p $zumisenv		[ -d ${zumisenv} ] \|\| mkdir -p ${zumisenv}
	cat $zumisdir/zUMIs-miniconda.parta* > $miniconda		cat ${zumisdir}/zUMIs-miniconda.parta* > ${miniconda}
	tar -xj --overwrite -f $miniconda -C $zumisenv		tar -xj --overwrite -f ${miniconda} -C ${zumisenv}
	fi		fi
	#activate zUMIs environment!		#activate zUMIs environment!
	unset PYTHONPATH		unset PYTHONPATH
	unset PYTHONHOME		unset PYTHONHOME
	source $zumisenv/bin/activate		source ${zumisenv}/bin/activate
	conda-unpack		conda-unpack
	fi		fi

	if grep -q 'zUMIs_directory:' $yaml		if grep -q 'zUMIs_directory:' ${yaml} ; then
	then		sed -i "s\|zUMIs_directory:.*\|zUMIs_directory: ${zumisdir}\|" ${yaml}
	sed -i "s\|zUMIs_directory:.*\|zUMIs_directory: $zumisdir\|" $yaml
	else		else
	echo "zUMIs_directory: $zumisdir" >> $yaml		echo "zUMIs_directory: ${zumisdir}" >> ${yaml}
	fi		fi

	$Rexc $zumisdir/checkyaml.R $yaml > $project.zUMIs_YAMLerror.log		${Rexc} ${zumisdir}/checkyaml.R ${yaml} > ${project}.zUMIs_YAMLerror.log
	iserror=`tail $project.zUMIs_YAMLerror.log -n1 \| awk '{print $2}'`		iserror=$(tail ${project}.zUMIs_YAMLerror.log -n1 \| awk '{print $2}')

	if [[ $iserror -eq 1 ]] ; then		if [[ ${iserror} -eq 1 ]] ; then
	echo "YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers."		echo "YAML file has an error. Look at the zUMIs_YAMLerror.log or contact developers."
	exit 1		exit 1
	fi		fi


	echo -e "\n\n You provided these parameters:		echo -e "\n\n You provided these parameters:
	YAML file: $yaml		YAML file: ${yaml_orig}
	zUMIs directory: $zumisdir		zUMIs directory: ${zumisdir}
	STAR executable $starexc		STAR executable ${starexc}
	samtools executable $samtoolsexc		samtools executable ${samtoolsexc}
	pigz executable $pigzexc		pigz executable ${pigzexc}
	Rscript executable $Rexc		Rscript executable ${Rexc}
	RAM limit: $mem_limit		RAM limit: ${mem_limit}
	zUMIs version $vers \n\n" \| tee "$outdir/$project.zUMIs_runlog.txt"		zUMIs version ${vers} \n\n" \| tee "${outdir}/${project}.zUMIs_runlog.txt"
	date		date

	#check for executables		#check for executables
	sam_exc_check=`which $samtoolsexc`		sam_exc_check=$(which ${samtoolsexc})
	pigz_exc_check=`which $pigzexc`		pigz_exc_check=$(which ${pigzexc})
	r_exc_check=`which $Rexc`		r_exc_check=$(which ${Rexc})
	star_exc_check=`which $starexc`		star_exc_check=$(which ${starexc})

	if [[ -z "$sam_exc_check" ]] \|\|		if [[ -z "${sam_exc_check}" ]] \|\|
	[[ -z "$pigz_exc_check" ]] \|\|		[[ -z "${pigz_exc_check}" ]] \|\|
	[[ -z "$r_exc_check" ]] \|\|		[[ -z "${r_exc_check}" ]] \|\|
	[[ -z "$star_exc_check" ]]		[[ -z "${star_exc_check}" ]] ; then
	then
	echo "One or more of your executables were not found. Please check back."		echo "One or more of your executables were not found. Please check back."
	exit 1		exit 1
	fi		fi

	# Check if the STAR version used for mapping and the one in the provided STAR index are the same		# Check if the STAR version used for mapping and the one in the provided STAR index are the same
	starver=`$starexc --version \| sed 's/STAR_//g' \| sed 's/\s+//g'`		starver=$(${starexc} --version \| sed 's/STAR_//g' \| sed 's/\s+//g')
	staridxver=`grep "versionGenome" $staridxdir/genomeParameters.txt \| awk '{print $2}' \| sed 's/\s+//g'`		staridxver=$(grep "versionGenome" ${staridxdir}/genomeParameters.txt \| awk '{print $2}' \| sed 's/\s+//g')

	if [[ "$starver" != "$staridxver" ]]; then		if [[ "${starver}" != "${staridxver}" ]] ; then
	echo "WARNING: The STAR version used for mapping is $starver and the STAR index was created using the version $staridxver. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR $starver."		echo "WARNING: The STAR version used for mapping is ${starver} and the STAR index was created using the version ${staridxver}. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR ${starver}."
	#exit 1		#exit 1
	fi		fi

	#create output folders		#create output folders
	outdir=`grep 'out_dir' $yaml \| awk '{print $2}'`		outdir=$(grep 'out_dir' ${yaml} \| awk '{print $2}')
	#[ -d $outdir ] \|\| mkdir $outdir		#[ -d ${outdir} ] \|\| mkdir ${outdir}
	[ -d $outdir/zUMIs_output/ ] \|\| mkdir -p $outdir/zUMIs_output/		[ -d ${outdir}/zUMIs_output/ ] \|\| mkdir -p ${outdir}/zUMIs_output/
	[ -d $outdir/zUMIs_output/expression ] \|\| mkdir -p $outdir/zUMIs_output/expression		[ -d ${outdir}/zUMIs_output/expression ] \|\| mkdir -p ${outdir}/zUMIs_output/expression
	[ -d $outdir/zUMIs_output/stats ] \|\| mkdir -p $outdir/zUMIs_output/stats		[ -d ${outdir}/zUMIs_output/stats ] \|\| mkdir -p ${outdir}/zUMIs_output/stats
	[ -d $outdir/zUMIs_output/.tmpMerge ] \|\| mkdir -p $outdir/zUMIs_output/.tmpMerge		[ -d ${outdir}/zUMIs_output/.tmpMerge ] \|\| mkdir -p ${outdir}/zUMIs_output/.tmpMerge

	if [[ ! -d $outdir ]]; then		if [[ ! -d ${outdir} ]] ; then
	mkdir -p $outdir		mkdir -p ${outdir}
	if [ $? -ne 0 ] ; then		if [ $? -ne 0 ] ; then
	echo "Please provide a valide output directory path."		echo "Please provide a valide output directory path."
	exit 1		exit 1
	fi		fi
	fi		fi

	if		if [[ "${whichStage}" == "Filtering" ]] ; then
	[[ "$whichStage" == "Filtering" ]]
	then
	echo "Filtering..."		echo "Filtering..."

	f=`cut -d' ' -f1 <(echo $fqfiles)` # the first fastq file to determine gzip status		f=$(cut -d' ' -f1 <(echo ${fqfiles})) # the first fastq file to determine gzip status
	fullsize=`stat -L --printf="%s" $f`		fullsize=$(stat -L --printf="%s" ${f})

	tmpMerge=$outdir/zUMIs_output/.tmpMerge/		tmpMerge=${outdir}/zUMIs_output/.tmpMerge/

	if [[ $f =~ \.gz$ ]]; then		if [[ ${f} =~ \.gz$ ]] ; then
	$pigzexc -dc $f \| head -n 4000000 \| $pigzexc > $tmpMerge/$project.1mio.check.fq.gz		${pigzexc} -dc ${f} \| head -n 4000000 \| ${pigzexc} > ${tmpMerge}/${project}.1mio.check.fq.gz
	smallsize=`stat --printf="%s" $tmpMerge/$project.1mio.check.fq.gz`		smallsize=$(stat --printf="%s" ${tmpMerge}/${project}.1mio.check.fq.gz)
	rm $tmpMerge/$project.1mio.check.fq.gz		rm ${tmpMerge}/${project}.1mio.check.fq.gz
	nreads=`expr $fullsize \* 1000000 / $smallsize`		nreads=$(expr ${fullsize} \* 1000000 / ${smallsize})

	for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $nreads & done		for i in ${fqfiles} ; do bash ${zumisdir}/splitfq.sh ${i} ${pigzexc} ${num_threads} ${tmpMerge} splitfqgz ${project} ${nreads} & done
	wait		wait
	pref=`basename $f .gz`		pref=$(basename ${f} .gz)
	l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" \| sed 's/.gz//'`		l=$(ls ${tmpMerge}${pref}* \| sed "s\|${tmpMerge}${pref}\|\|" \| sed 's/.gz//')
	else		else
	cat $f \| head -n 4000000 > $tmpMerge/$project.1mio.check.fq		cat ${f} \| head -n 4000000 > ${tmpMerge}/${project}.1mio.check.fq
	smallsize=`stat --printf="%s" $tmpMerge/$project.1mio.check.fq`		smallsize=$(stat --printf="%s" ${tmpMerge}/${project}.1mio.check.fq)
	rm $tmpMerge/$project.1mio.check.fq		rm ${tmpMerge}/${project}.1mio.check.fq
	nreads=`expr $fullsize \* 1000000 / $smallsize`		nreads=$(expr ${fullsize} \* 1000000 / ${smallsize})

	for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $nreads & done		for i in ${fqfiles} ; do bash ${zumisdir}/splitfq.sh ${i} ${pigzexc} ${num_threads} ${tmpMerge} splitfq ${project} ${nreads} & done
	wait		wait
	pref=`basename $f`		pref=$(basename ${f})
	l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|"`		l=$(ls ${tmpMerge}${pref}* \| sed "s\|${tmpMerge}${pref}\|\|")
	fi		fi

	for x in $l; do perl $zumisdir/fqfilter_v2.pl $yaml $samtoolsexc $Rexc $pigzexc $zumisdir $x & done		for x in ${l} ; do perl ${zumisdir}/fqfilter_v2.pl ${yaml} ${samtoolsexc} ${Rexc} ${pigzexc} ${zumisdir} ${x} & done
	wait		wait
	bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml $samtoolsexc		bash ${zumisdir}/mergeBAM.sh ${zumisdir} ${tmpMerge} ${num_threads} ${project} ${outdir} ${yaml} ${samtoolsexc}
	for i in $fqfiles; do		for i in ${fqfiles} ; do
	pref=`basename $i \| sed 's/.fastq.gz//' \| sed 's/.fq.gz//'`		pref=$(basename ${i} \| sed 's/.fastq.gz//' \| sed 's/.fq.gz//')
	rm $tmpMerge$pref*gz		rm ${tmpMerge}${pref}*gz
	done		done
	date		date

	#run barcode detection		#run barcode detection
	$Rexc $zumisdir/zUMIs-BCdetection.R $yaml		${Rexc} ${zumisdir}/zUMIs-BCdetection.R ${yaml}

	#check if BC correction should be performed!		#check if BC correction should be performed!
	BCbinTable=$outdir/zUMIs_output/"$project".BCbinning.txt		BCbinTable=${outdir}/zUMIs_output/"${project}".BCbinning.txt
	if [[ -f "$BCbinTable" ]]; then		if [[ -f "${BCbinTable}" ]] ; then
	for x in $l; do		for x in ${l} ; do
	rawbam="$tmpMerge/$project.$x.raw.tagged.bam"		rawbam="${tmpMerge}/${project}.${x}.raw.tagged.bam"
	fixedbam="$tmpMerge/$project.$x.filtered.tagged.bam"		fixedbam="${tmpMerge}/${project}.${x}.filtered.tagged.bam"
	mv $fixedbam $rawbam		mv ${fixedbam} ${rawbam}
	perl $zumisdir/correct_BCtag.pl $rawbam $fixedbam $BCbinTable $samtoolsexc &		perl ${zumisdir}/correct_BCtag.pl ${rawbam} ${fixedbam} ${BCbinTable} ${samtoolsexc} &
	done		done
	wait		wait
	fi		fi
	@@ -281,44 +284,40 @@ then
	fi		fi

	if		if
	[[ "$whichStage" == "Filtering" ]] \|\|		[[ "${whichStage}" == "Filtering" ]] \|\|
	[[ "$whichStage" == "Mapping" ]]		[[ "${whichStage}" == "Mapping" ]] ; then
	then
	echo "Mapping..."		echo "Mapping..."
	$Rexc $zumisdir/zUMIs-mapping.R $yaml		${Rexc} ${zumisdir}/zUMIs-mapping.R ${yaml}
	date		date
	fi		fi

	if		if
	[[ "$whichStage" == "Filtering" ]] \|\|		[[ "${whichStage}" == "Filtering" ]] \|\|
	[[ "$whichStage" == "Mapping" ]] \|\|		[[ "${whichStage}" == "Mapping" ]] \|\|
	[[ "$whichStage" == "Counting" ]]		[[ "${whichStage}" == "Counting" ]] ; then
	then
	echo "Counting..."		echo "Counting..."
	$Rexc $zumisdir/zUMIs-dge2.R $yaml		${Rexc} ${zumisdir}/zUMIs-dge2.R ${yaml}
	date		date
	$Rexc $zumisdir/misc/rds2loom.R $yaml		${Rexc} ${zumisdir}/misc/rds2loom.R ${yaml}
	date		date
	if [[ "$velo" == "yes" ]]; then		if [[ "${velo}" == "yes" ]] ; then
	$Rexc $zumisdir/runVelocyto.R $yaml		${Rexc} ${zumisdir}/runVelocyto.R ${yaml}
	fi		fi
	fi		fi

	if		if
	[[ "$whichStage" == "Filtering" ]] \|\|		[[ "${whichStage}" == "Filtering" ]] \|\|
	[[ "$whichStage" == "Mapping" ]] \|\|		[[ "${whichStage}" == "Mapping" ]] \|\|
	[[ "$whichStage" == "Counting" ]] \|\|		[[ "${whichStage}" == "Counting" ]] \|\|
	[[ "$whichStage" == "Summarising" ]]		[[ "${whichStage}" == "Summarising" ]] ; then
	then		if [[ "${isstats}" == "yes" ]] ; then
	if [[ "$isstats" == "yes" ]]; then
	echo "Descriptive statistics..."		echo "Descriptive statistics..."
	$Rexc $zumisdir/zUMIs-stats2.R $yaml		${Rexc} ${zumisdir}/zUMIs-stats2.R ${yaml}
	fi		fi
	date		date
	fi		fi


	#close conda enviroment if necessary		#close conda enviroment if necessary
	if [[ $conda = true ]]; then		if [[ ${conda} = true ]] ; then
	source $zumisenv/bin/deactivate		source ${zumisenv}/bin/deactivate
	fi		fi

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