Update juicer.sh (063d0465) · Commits · Chaos / chaos.juicer

CPU/juicer.sh

+18 −16

Original line number	Diff line number	Diff line
		@@ -238,7 +238,8 @@ fastqdir=${topDir}"/fastq/_R.fastq*"
		outputdir=${topDir}"/aligned"
		tmpdir=${topDir}"/HIC_tmp"

		## Check that fastq directory exists and has proper fastq files
		## Check that fastq directory exists and has proper fastq files; only if necessary
		if [[ -z "$final" && -z "$dedup" && -z "$postproc" && -z "$deduponly" && -z "$merge" && -z "$mergeonly" ]]; then
		if [ ! -d "$topDir/fastq" ]; then
		echo "Directory \"$topDir/fastq\" does not exist."
		echo "Create \"$topDir/fastq\" and put fastq files to be aligned there."
		@@ -256,6 +257,7 @@ else
		fi
		fi
		fi
		fi

		## Create output directory, only if not in dedup, final, or postproc stages
		if [[ -d "$outputdir" && -z "$final" && -z "$dedup" && -z "$postproc" && -z "$deduponly" ]]
		@@ -264,7 +266,7 @@ then
		echo "***! Type \"juicer.sh -h \" for help"
		exit 1
		else
		if [[ -z "$final" && -z "$dedup" && -z "$postproc" && -z "$deduponly" ]]; then
		if [[ -z "$final" && -z "$dedup" && -z "$postproc" && -z "$deduponly" && -z "$alignonly" ]]; then
		mkdir "$outputdir" \|\| { echo "***! Unable to create ${outputdir}, check permissions." ; exit 1; }
		fi
		fi