minor changes on --verbose (b12f3d3b) · Commits · github_fork / Universc

launch_universc.sh

+19 −19

Original line number	Diff line number	Diff line
		@@ -1489,7 +1489,7 @@ echo ""


		####setup whitelist#####
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "lock $lock"
		fi
		if [[ $lock -eq 0 ]]; then
		@@ -1635,10 +1635,10 @@ if [[ $lock -eq 0 ]]; then

		echo "verbose $verbose"
		#change last call file
		#if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "Setting last call as..."
		echo "${barcodelength} ${umilength} ${barcodefile}"
		#fi
		fi
		echo "${barcodelength} ${umilength} ${barcodefile}" > $lastcallfile

		cd - > /dev/null
		@@ -1691,7 +1691,7 @@ fi

		crR1s=()
		for fq in "${read1[@]}"; do
		if [[ $verbose == true ]]; then
		if [[ $verbose ]]; then
		echo $fq
		fi
		to=`basename $fq`
		@@ -1753,7 +1753,7 @@ for fq in "${read2[@]}"; do

		echo " handling $fq ..."
		if [[ ! -f $to ]] \|\| [[ $convert == "true" ]]; then
		if [[ $verbose == true ]]; then
		if [[ $verbose ]]; then
		echo "cp -f $fq $to";
		fi
		cp -f $fq $to
		@@ -1762,7 +1762,7 @@ done

		if [[ ${#index1[@]} -ge 1 ]]; then
		crI1s=()
		if [[ $verbose == true ]]; then
		if [[ $verbose ]]; then
		echo "Processing Index"
		echo "Fastqs: ${index1[@]}"
		echo "${index1[@]}"
		@@ -1819,7 +1819,7 @@ if [[ ${#index2[@]} -ge 1 ]]; then
		to=`echo $to \| sed -e "s/_R3_/_I2_/g"`
		fi

		if [[ $verbose == true ]]; then
		if [[ $verbose ]]; then
		echo "$to"
		fi
		crI2s+=($to)
		@@ -1844,7 +1844,7 @@ if [[ $convert == "false" ]]; then
		else
		echo " adjustment parameters:"
		echo " barcodes: ${barcodeadjust}bps at its head"
		echo " UMIs: ${umiadjust}bps at its tail"
		echo " UMiIs: ${umiadjust}bps at its tail"

		echo " making technology-specific modifications ..."
		#CEL-Seq2: swap barcode and UMI
		@@ -2065,17 +2065,17 @@ echo ""
		echo "#####cellranger command#####"

		start=`date +%s`
		echo "cellranger count --id=$id \
		--fastqs=$crIN \
		--lanes=$LANE \
		--r1-length=$totallength \
		--chemistry=$chemistry \
		--transcriptome=$reference \
		--sample=$SAMPLE \
		$d \
		$n \
		$j \
		$l \
		echo "cellranger count --id=$id
		--fastqs=$crIN
		--lanes=$LANE
		--r1-length=$totallength
		--chemistry=$chemistry
		--transcriptome=$reference
		--sample=$SAMPLE
		$d
		$n
		$j
		$l
		$m
		"
		echo "##########"

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