add presets for testrun of each technology (9a3f470f) · Commits · github_fork / Universc

launch_universc.sh

+26 −0

Original line number	Diff line number	Diff line
		@@ -101,6 +101,7 @@ crIN=input4cellranger #name of the directory with all FASTQ files given to cellr

		#variable options
		setup=false
		testrun=false
		convert=true
		read1=()
		read2=()
		@@ -136,6 +137,11 @@ for op in "$@"; do
		next=false
		shift
		;;
		--testrun)
		testrun=true
		next=false
		shift
		;;
		-t\|--technology)
		shift
		if [[ $1 != "" ]]; then
		@@ -336,6 +342,26 @@ if [[ "$technology" != "10x" ]] && [[ "$technology" != "nadia" ]] && [[ "$techno
		exit 1
		fi

		if [[ $testrun == "true" ]]; then
		reference=${SDRI}/test/cellranger_reference/cellranger-tiny-ref/3.0.0"
		if [[ -z $id ]] then
		id=test-tiny-${technology}
		fi
		if [[ $technology == "10x" ]]; then
		gunzip -k ${SDIR}test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L00[12]_R[12]_001.fastq.gz
		read1=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_001.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq")
		read2=("test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R1_002.fastq" "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq")
		elif [[ $technology == "nadia" ]]; then
		gunzip -k test/shared/dropseq-test/SRR1873277_S1_L001_R[12]_001.fastq
		read1=("test/shared/dropseq-test/SRR1873277_S1_L001_R1_001.fastq")
		read2=("test/shared/dropseq-test/SRR1873277_S1_L001_R2_001.fastq")
		elif [[ $technology == "icell8" ]]; then
		gunzip -k test/shared/mappa-test/test_FL_R[12].fastq.gz
		read1=("test/shared/mappa-test/test_FL_R1.fastq)
		read2=("test/shared/mappa-test/test_FL_R2.fastq")
		fi
		fi

		#check for presence of read1 and read2 files
		if [[ $setup == "false" ]]; then
		if [[ ${#read1[@]} -eq 0 ]]; then

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