update R3 and R4 input (0355b9e2) · Commits · github_fork / Universc

launch_universc.sh

+59 −4

Original line number	Diff line number	Diff line
		@@ -1055,6 +1055,7 @@ if [[ $setup == "false" ]]; then
		r1_list=("${read1[@]}")
		r2_list=("${read2[@]}")
		i1_list=()
		r4_list=()
		for j in ${!r1_list[@]}; do
		read=${r1_list[$j]}
		R1_file=$read
		@@ -1123,6 +1124,7 @@ if [[ $setup == "false" ]]; then
		fi
		r1_list=("${read1[@]}")
		r2_list=("${read2[@]}")
		r3_list=()
		i2_list=()
		for j in ${!r1_list[@]}; do
		read=${r1_list[$j]}
		@@ -1136,9 +1138,14 @@ if [[ $setup == "false" ]]; then
		if [[ $verbose ]]; then
		echo " file $R3_file found, replacing $I2_file ..."
		fi
		if [[ $technology == "10x" ]]; then
		r3_read=$R3_file
		r3_list[$j]=$r3_read
		else
		i2_read=$R3_file
		i2_list[$j]=$r3_read
		fi
		fi
		if [[ -f $I2_file ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'.gz') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'.fastq') ]] \|\| [[ -f $(find $(dirname ${read}) -name $(basename ${I2_file})'*.fq') ]]; then
		i2_present="true"
		if [[ $verbose ]]; then
		@@ -1159,6 +1166,12 @@ if [[ $setup == "false" ]]; then
		echo " index files found ${#index2[@]} I2s: ${index2[@]}"
		fi
		fi
		if [[ ${#r3_list[@]} -gt 0 ]]; then
		read3=("${r3_list[@]}")
		if [[ $verbose ]]; then
		echo " index files found ${#read3[@]} R3s: ${read3[@]}"
		fi
		fi
		fi
		fi
		elif [[ ${#index2[@]} -gt 0 ]]; then
		@@ -1169,9 +1182,15 @@ if [[ $setup == "false" ]]; then
		fi

		if [[ $verbose ]]; then
		echo " Input files prost-curation 1"
		echo " Input files post-curation 1"
		echo " ${#read1[@]}files - read1s: ${read1[@]}"
		echo " ${#read2[@]}files - read2s: ${read2[@]}"
		if [[ ${#index1[@]} -gt 0 ]]; then
		echo " ${#read3[@]}files - R3s: ${read3[@]}"
		fi
		if [[ ${#index2[@]} -gt 0 ]]; then
		echo " ${#read4[@]}files - R4s: ${read4[@]}"
		fi
		if [[ ${#index1[@]} -gt 0 ]]; then
		echo " ${#index1[@]}files - I1s: ${index1[@]}"
		fi
		@@ -1181,11 +1200,17 @@ if [[ $verbose ]]; then
		echo " number of these files are as expected"
		fi



		keys=("R1" "R2")
		if [[ $r3_present == "true" ]]; then
		keys=(${keys[@]} "R3")
		if [[ $technology == "10x" ]]; then
		read3=("${read3[@]}")
		else
		read3=("${index2[@]}")
		fi
		fi
		if [[ $r4_present == "true" ]]; then
		keys=(${keys[@]} "R4")
		read4=("${index1[@]}")
		@@ -2765,6 +2790,36 @@ if [[ ${#index2[@]} -ge 1 ]]; then
		fi
		done
		fi

		if [[ ${#read3[@]} -ge 1 ]]; then
		crR3s=()
		if [[ $verbose ]]; then
		echo "Processing Index"
		echo "Fastqs: ${read3[@]}"
		echo "${read3[@]}"
		fi
		for fq in "${read3[@]}"; do
		if [[ $verbose ]]; then
		echo "$fq"
		fi
		to=`basename $fq`
		to="${crIN}/${to}"
		to=$(echo "$to" \| sed 's/\.gz$//')

		if [[ $verbose ]]; then
		echo "$to"
		fi
		crR3s+=($to)

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

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