create output folder correctly (59c39a76) · Commits · github_fork / ZUMIs

zUMIs.sh

+9 −8

Original line number	Diff line number	Diff line
		@@ -3,7 +3,7 @@
		# Pipeline to run UMI-seq analysis from fastq to read count tables.
		# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann
		# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se
		vers=2.9.3b
		vers=2.9.3c
		currentv=$(curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/main/zUMIs.sh \| grep '^vers=' \| cut -f2 -d "=")
		if [ "$currentv" != "$vers" ] ; then
		echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------";
		@@ -176,6 +176,14 @@ if [[ ${iserror} -eq 1 ]] ; then
		exit 1
		fi

		#create main output folder if it didn't exist
		if [[ ! -d ${outdir} ]] ; then
		mkdir -p ${outdir}
		if [ $? -ne 0 ] ; then
		echo "Please provide a valid output directory path."
		exit 1
		fi
		fi

		echo -e "\n\n You provided these parameters:
		YAML file: ${yaml_orig}
		@@ -219,13 +227,6 @@ outdir=$(grep 'out_dir' ${yaml} \| awk '{print $2}')
		[ -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
		echo "Filtering..."