single core test jobs (0a90e1c9) · Commits · github_fork / Universc

test/run_tests_10x.sh

+9 −4

Original line number	Diff line number	Diff line
		@@ -46,7 +46,9 @@ if [[ -d tiny-test ]]; then
		rm -rf tiny-test
		fi
		# test cellranger call
		if [[ $cellrangerversion == "3.0.2" ]]; then
		cellranger testrun --id="tiny-test"
		fi
		# unzip input data
		if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz ]]; then
		gunzip -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz
		@@ -66,7 +68,8 @@ if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcode
		fi
		cellranger count --id="tiny-count-v3" \
		--fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0"
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--jobmode "local" --localcores 1
		if [[ -d tiny-count-v2 ]]; then
		rm -rf tiny-count-v2
		fi
		@@ -78,7 +81,8 @@ if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcode
		fi
		cellranger count --id="tiny-count-v2" \
		--fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0"
		--transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0" \
		--jobmode "local" --localcores 1

		# call convert on 10x with multiple lanes
		if [[ -d test-10x-v3 ]]; then
		@@ -97,7 +101,8 @@ fi
		bash launch_universc.sh --id "test-10x-v3" --technology "10x" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--file "test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001" \
		"test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002"
		"test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002" \
		--jobmode "local" --localcores 1

		# compress all input files
		if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then

test/run_tests_dropseq.sh

+2 −1

Original line number	Diff line number	Diff line
		@@ -41,7 +41,8 @@ fi
		bash launch_universc.sh --id "test-dropseq" --technology "nadia" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--read1 "test/shared/dropseq-test/SRR1873277_Sample1_R1" \
		--read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2"
		--read2 "test/shared/dropseq-test/SRR1873277_Sample1_R2" \
		--jobmode "local" --localcores 1

		# reset test data (compress)
		if [[ -f test/shared/dropseq-test/SRR1873277_Sample1_S1_L001_R1_001.fastq ]]; then

test/run_tests_icell8.sh

+2 −2

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-2-lanes" --technology "iCe
		--read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R1_001.fastq" \
		--read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" "test/shared/icell8-test/72618_KU812_L002_R2_001.fastq" \
		--barcodefile "test/shared/icell8-test/WellList.txt" \
		--jobmode "local"
		--jobmode "local" --localcores 1
		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
		fi
		@@ -61,7 +61,7 @@ bash launch_universc.sh --id "test-icell8-72618_KU812-1-lane" --technology "iCel
		--read1 "test/shared/icell8-test/72618_KU812_L001_R1_001.fastq" \
		--read2 "test/shared/icell8-test/72618_KU812_L001_R2_001.fastq" \
		--barcodefile "test/shared/icell8-test/WellList.txt" \
		--jobmode "local"
		--jobmode "local" --localcores 1
		if [ -f test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq ]; then
		rename "s/_S1_L001/_L001/" test/shared/icell8-test/72618_KU812_S1_L001_R1_001.fastq*
		fi

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