update smartseq3 tests for TSO and dual indexes (4cdc8d7a) · Commits · github_fork / Universc

test/run_tests_smartseq3_local.sh

+10 −8

Original line number	Diff line number	Diff line
		@@ -20,14 +20,16 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[
		fi

		# compress all input files
		if [[ -f test/shared/smartseq3-test/*fastq ]]; then
		if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_R1.fastq ]]; then
		gzip test/shared/smartseq3-test/*fastq
		fi

		mv test/shared/smartseq3-test/Smartseq3_diySpike5_S1_L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike5_S1_R1.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike5_S1_L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike5_S1_R2.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike5_S1_L001_I1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike5_S1_I1.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike5_S1_L001_I2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike5_S1_I2.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_S1_R1.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_S1_R2.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_S1_I1.fastq.gz
		mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_S1_I2.fastq.gz
		rename -f "s/_S1_L001/_L001/" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12].fastq.gz
		rename -f "s/_S1//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_[IR][12].fastq.gz

		# test manual setup
		bash launch_universc.sh -t "smartseq3" --setup
		@@ -39,8 +41,8 @@ if [[ -d test-smartseq3 ]]; then
		rm -rf test-smartseq3
		fi

		if [[ ! -f ${whitelistdir}/SmartSeq3_test_barcodes.txt ]]; then
		gunzip -k ${whitelistdir}/SmartSeq3_test_barcodes.txt.gz
		if [[ ! -f whitelists/SmartSeq3_test_barcodes.txt ]]; then
		gunzip -k whitelists/SmartSeq3_test_barcodes.txt.gz
		fi

		# call on smartseq3 with files
		@@ -48,7 +50,7 @@ bash launch_universc.sh --id "test-smartseq3" --technology "smartseq3" \
		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
		--read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \
		--read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \
		--barcodefile "${whitelistdir}/SmartSeq3_test_barcodes.txt" \
		--barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \
		--per-cell-data --jobmode "local" --localcores 1

		if [ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz ]; then