debug passing reads to input directory (9634fc4d) · Commits · github_fork / Universc

launch_universc.sh

+40 −18

Original line number	Diff line number	Diff line
		@@ -388,7 +388,7 @@ done


		#####check if input maches expected formats#####
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "checking options ..."
		fi

		@@ -585,7 +585,7 @@ for i in {1..2}; do

		for j in ${!list[@]}; do
		read=${list[$j]}
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "checking file format for $read ..."
		fi
		if [[ -f $read ]] && [[ -h $read ]]; then
		@@ -624,7 +624,7 @@ for i in {1..2}; do
		exit 1
		fi

		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo " $read"
		fi

		@@ -650,13 +650,13 @@ for i in {1..2}; do

		for j in ${!list[@]}; do
		read=${list[$j]}
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo " checking file name for $read ..."
		fi

		if [[ -h $read ]]; then
		path=`readlink -f $read`
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo " *Warning: file $read not in current directory. Path to the file captured instead.*"
		echo " (file) $read"
		echo " (path) $path"
		@@ -666,13 +666,13 @@ for i in {1..2}; do
		case $read in
		#check if contains lane before read
		_L0[0123456789][0123456789]_$readkey)
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo " $read compatible with lane"
		fi
		;;
		*)
		#rename file
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "*Warning: file $read does not have lane value in its name. Lane 1 is assumed.*"
		echo " renaming $read ..."
		fi
		@@ -685,13 +685,13 @@ for i in {1..2}; do
		case $read in
		#check if contains sample before lane
		_S[0123456789]_L0)
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo " $read compatible with sample"
		fi
		;;
		*)
		#rename file
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "*Warning: file $read does not have sample value in its name. Sample $k is assumed.*"
		echo " renaming $read ..."
		fi
		@@ -705,13 +705,13 @@ for i in {1..2}; do
		case $read in
		#check if contains sample before lane
		_${readkey}_001.)
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo " $read compatible with suffix"
		fi
		;;
		*)
		#rename file
		if [[ $verbose == "true" ]]; then
		if [[ $verbose ]]; then
		echo "*Warning: file $read does not have suffix in its name. Suffix 001 is given.*"
		echo " renaming $read ..."
		fi
		@@ -1178,7 +1178,7 @@ fi


		#####exiting when setup is all that is requested#####
		if [[ $setup == "ture" ]]; then
		if [[ $setup == "true" ]]; then
		lock=`cat $lockfile`
		lock=$(($lock-1))
		echo $lock > $lockfile
		@@ -1200,15 +1200,26 @@ else
		echo " directory $crIN already exists"
		fi


		if [[ $verbose == true ]]; then
		echo "convert: $convert"
		fi
		if [[ $convert == "true" ]]; then
		echo "moving file to new location"
		fi


		crR1s=()

		if [[ $verbose == true ]]; then
		echo "Processing Read1"
		echo "Fastqs: ${read1[@]}"
		fi
		if [[ $verbose == true ]]; then
		echo "${read1[@]}"
		fi
		for fq in "${read1[@]}"; do
		if [[ $verbose == true ]]; then echo $fq; fi
		to=`basename $fq`
		to="${crIN}/${to}"

		@@ -1216,13 +1227,16 @@ for fq in "${read1[@]}"; do
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#where converted "read1" is R2 in source files (corrected names for cellranger)
		echo "using transcripts in Read 2 for ${technology}"
		to=`echo $to \| sed -e "s/_R2_/_R1_/g"
		to=`echo $to \| sed -e "s/_R2_/_R1_/g"`
		fi


		if [[ $verbose == true ]]; then echo $to; fi
		crR1s+=($to)

		echo " handling $fq ..."
		if [[ ! -f $to ]] \|\| [[ $convert == "true" ]]; then
		if [[ $verbose == true ]]; then echo "cp -f $fq $to"; fi
		cp -f $fq $to
		fi
		if [[ $convert == "true" ]]; then
		@@ -1231,10 +1245,16 @@ for fq in "${read1[@]}"; do
		done

		crR2s=()

		if [[ $verbose == true ]]; then
		echo "Processing Read2"
		echo "Fastqs: ${read2[@]}"
		fi
		if [[ $verbose == true ]]; then
		echo "${read2[@]}"
		fi
		for fq in "${read2[@]}"; do
		if [[ $verbose == true ]]; then echo "$fq"; fi
		to=`basename $fq`
		to="${crIN}/${to}"
		to=$(echo "$to" \| sed 's/\.gz$//')
		@@ -1243,13 +1263,15 @@ for fq in "${read2[@]}"; do
		if [[ "$technology" == "indrop-v2" ]] \|\| [[ "$technology" == "indrop-v3" ]]; then
		#where converted "read2" is R1 in source files
		echo "using transcripts in Read 1 for ${technology}"
		to=`echo $to \| sed -e "s/_R1_/_R2_/g"
		to=`echo $to \| sed -e "s/_R1_/_R2_/g"`
		fi

		if [[ $verbose == true ]]; then echo "$to"; fi
		crR2s+=($to)

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

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