copy files only if missing or --keep not specified (6cc3a7cb) · Commits · github_fork / Universc

launch_universc.sh

+22 −2

Original line number	Diff line number	Diff line
		@@ -776,9 +776,19 @@ for fq in "${read1[@]}"; do
		if [[ $fq == *'.gz' ]]; then
		echo " unzipping and redirecting $fq file..."
		gunzip -c $fq > $to
		else
		elif [ ! keep ]
		echo " redirecting $fq file..."
		cp $fq $to
		else
		if [ -f $crIN/$read ]
		then
		echo " converted $fq file exists"
		else
		echo " converted $fq file does not exist"
		cp $fq $to
		convert=true
		echo " warning: file will be converted"
		fi
		fi
		done

		@@ -792,9 +802,19 @@ for fq in "${read2[@]}"; do
		if [[ $fq == *'.gz' ]]; then
		echo " unzipping and redirecting $fq file..."
		gunzip -c $fq > $to
		else
		elif [ ! keep ]
		echo " redirecting $fq file..."
		cp $fq $to
		else
		if [ -f $crIN/$read ]
		then
		echo " converted $fq file exists"
		else
		echo " converted $fq file does not exist"
		cp $fq $to
		convert=true
		echo " warning: file will be converted"
		fi
		fi
		done