Create temporary 'corrected' YAML file for default options, so that input file is not overwritten (0613b35c) · Commits · github_fork / ZUMIs

checkyaml.R

+37 −32

Original line number	Diff line number	Diff line
		#!/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)

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


		@@ -60,7 +63,8 @@ print(
		function(x) {
		if(is.null(unlist(inp$sequence_files[[x]]$name))) {
		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("")}
		})
		))
		@@ -70,7 +74,8 @@ print(
		function(x) {
		if(is.null(unlist(inp$sequence_files[[x]]$base_definition))) {
		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(any(!grepl("^BC\|^UMI\|^cDNA",x$base_definition))) {
		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	Diff line number	Diff line
		@@ -4,16 +4,18 @@
		# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
		# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se
		vers=2.8.2
		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
		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

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

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

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

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

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

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

		zUMIs version $vers
		zUMIs version ${vers}

		EOF
		}

		# 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.
		case $options in
		y ) yaml=$OPTARG;;
		d ) zumisdir=$OPTARG;;
		case ${options} in
		y ) yaml=${OPTARG};;
		d ) zumisdir=${OPTARG};;
		c ) conda=true;;
		h ) usage
		exit 1;;
		\? ) echo -e "\n This key is not available! Please check the usage again: -$OPTARG"
		\? ) echo -e "\n This key is not available! Please check the usage again: -${OPTARG}"
		usage
		exit 1;;
		esac
		done

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

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

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

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


		if grep -q 'samtools_exec:' $yaml
		then
		samtoolsexc=`grep 'samtools_exec' $yaml \| awk '{print $2}'`
		num_threads=$(grep 'num_threads' ${yaml} \| awk '{print $2}')
		project=$(grep 'project:' ${yaml} \| awk '{print $2}')
		whichStage=$(grep 'which_Stage:' ${yaml} \| awk '{print $2}')
		outdir=$(grep 'out_dir' ${yaml} \| awk '{print $2}')
		genomedir=$(grep 'STAR_index:' ${yaml} \| awk '{print $2}')
		mem_limit=$(grep 'mem_limit:' ${yaml} \| awk '{print $2}')
		isstats=$(grep 'make_stats:' ${yaml} \| awk '{print $2}')
		fqfiles=$(grep 'name:' ${yaml} \| awk '{print $2}')
		velo=$(grep 'velocyto:' ${yaml} \| awk '{print $2}')
		staridxdir=$(grep 'STAR_index:' ${yaml} \| awk '{print $2}')


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

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

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

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

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

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

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

		$Rexc $zumisdir/checkyaml.R $yaml > $project.zUMIs_YAMLerror.log
		iserror=`tail $project.zUMIs_YAMLerror.log -n1 \| awk '{print $2}'`
		${Rexc} ${zumisdir}/checkyaml.R ${yaml} > ${project}.zUMIs_YAMLerror.log
		iserror=$(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."
		exit 1
		fi


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

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

		if [[ -z "$sam_exc_check" ]] \|\|
		[[ -z "$pigz_exc_check" ]] \|\|
		[[ -z "$r_exc_check" ]] \|\|
		[[ -z "$star_exc_check" ]]
		then
		sam_exc_check=$(which ${samtoolsexc})
		pigz_exc_check=$(which ${pigzexc})
		r_exc_check=$(which ${Rexc})
		star_exc_check=$(which ${starexc})

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

		# 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'`
		staridxver=`grep "versionGenome" $staridxdir/genomeParameters.txt \| awk '{print $2}' \| sed 's/\s+//g'`
		starver=$(${starexc} --version \| sed 's/STAR_//g' \| sed 's/\s+//g')
		staridxver=$(grep "versionGenome" ${staridxdir}/genomeParameters.txt \| awk '{print $2}' \| sed 's/\s+//g')

		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 $starver."
		if [[ "${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}."
		#exit 1
		fi

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

		if [[ ! -d $outdir ]]; then
		mkdir -p $outdir
		outdir=$(grep 'out_dir' ${yaml} \| awk '{print $2}')
		#[ -d ${outdir} ] \|\| mkdir ${outdir}
		[ -d ${outdir}/zUMIs_output/ ] \|\| mkdir -p ${outdir}/zUMIs_output/
		[ -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/.tmpMerge ] \|\| mkdir -p ${outdir}/zUMIs_output/.tmpMerge

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

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

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

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

		if [[ $f =~ \.gz$ ]]; then
		$pigzexc -dc $f \| head -n 4000000 \| $pigzexc > $tmpMerge/$project.1mio.check.fq.gz
		smallsize=`stat --printf="%s" $tmpMerge/$project.1mio.check.fq.gz`
		rm $tmpMerge/$project.1mio.check.fq.gz
		nreads=`expr $fullsize \* 1000000 / $smallsize`
		if [[ ${f} =~ \.gz$ ]] ; then
		${pigzexc} -dc ${f} \| head -n 4000000 \| ${pigzexc} > ${tmpMerge}/${project}.1mio.check.fq.gz
		smallsize=$(stat --printf="%s" ${tmpMerge}/${project}.1mio.check.fq.gz)
		rm ${tmpMerge}/${project}.1mio.check.fq.gz
		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
		pref=`basename $f .gz`
		l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" \| sed 's/.gz//'`
		pref=$(basename ${f} .gz)
		l=$(ls ${tmpMerge}${pref}* \| sed "s\|${tmpMerge}${pref}\|\|" \| sed 's/.gz//')
		else
		cat $f \| head -n 4000000 > $tmpMerge/$project.1mio.check.fq
		smallsize=`stat --printf="%s" $tmpMerge/$project.1mio.check.fq`
		rm $tmpMerge/$project.1mio.check.fq
		nreads=`expr $fullsize \* 1000000 / $smallsize`
		cat ${f} \| head -n 4000000 > ${tmpMerge}/${project}.1mio.check.fq
		smallsize=$(stat --printf="%s" ${tmpMerge}/${project}.1mio.check.fq)
		rm ${tmpMerge}/${project}.1mio.check.fq
		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
		pref=`basename $f`
		l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|"`
		pref=$(basename ${f})
		l=$(ls ${tmpMerge}${pref}* \| sed "s\|${tmpMerge}${pref}\|\|")
		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
		bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml $samtoolsexc
		for i in $fqfiles; do
		pref=`basename $i \| sed 's/.fastq.gz//' \| sed 's/.fq.gz//'`
		rm $tmpMerge$pref*gz
		bash ${zumisdir}/mergeBAM.sh ${zumisdir} ${tmpMerge} ${num_threads} ${project} ${outdir} ${yaml} ${samtoolsexc}
		for i in ${fqfiles} ; do
		pref=$(basename ${i} \| sed 's/.fastq.gz//' \| sed 's/.fq.gz//')
		rm ${tmpMerge}${pref}*gz
		done
		date

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

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

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

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

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


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

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