Merge branch 'master' into dev (8ac7bc55) · Commits · github_fork / Universc

.github/workflows/docker-run-tests.yml

+1 −0

Original line number	Original line	Diff line number	Diff line


	name: Run all tests in Docker		name: Run all tests in Docker
	on: push		on: push
	jobs:		jobs:

.github/workflows/docker-test-smartseq3.yml

+4 −4

Original line number	Original line	Diff line number	Diff line
	name: Test Smart-Seq3		name: Test ICELL8
	on: push		on: push
	jobs:		jobs:
	test:		test:
	@@ -10,7 +10,7 @@ jobs:
	- name: Status		- name: Status
	run: echo "build complete"		run: echo "build complete"

	test-smart-seq3:		test-smartseq3:
	runs-on: ubuntu-20.04		runs-on: ubuntu-20.04
	steps:		steps:
	- uses: actions/checkout@v2		- uses: actions/checkout@v2
	@@ -30,5 +30,5 @@ jobs:
	push: false		push: false
	- name: clear environment		- name: clear environment
	run: rm -rf *		run: rm -rf *
	- name: Test Smart-Seq3		- name: Test ICELL8
	run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m bash /universc/test/run_tests_smartseq3_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 15m bash /universc/test/run_tests_smartseq3_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

Makefile

+4 −1

Original line number	Original line	Diff line number	Diff line
	@@ -5,7 +5,7 @@ export ROOT_DIR=$(shell pwd)

	# Targets for development builds.		# Targets for development builds.
	#		#
	all: reference		all: reference test-data

	clean: reference-clean manual-clean		clean: reference-clean manual-clean

	@@ -18,6 +18,9 @@ PYTHON_SITE_PKG:=$(lastword $(wildcard $(PYTHON_LIB_DIR)/python*/site-packages))
	PYTHON_CFLAGS:=$(shell python-config --cflags)		PYTHON_CFLAGS:=$(shell python-config --cflags)
	PYTHON_LDFLAGS:=$(shell python-config --ldflags)		PYTHON_LDFLAGS:=$(shell python-config --ldflags)

			test-data:
			make -C test/shared/smartseq3-test

	reference:		reference:
	make -C test/cellranger_reference/cellranger-tiny-ref		make -C test/cellranger_reference/cellranger-tiny-ref

test/run_tests_smartseq3_gh_actions.sh

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -26,7 +26,7 @@ if [[ -f test/shared/smartseq3-test/*fastq ]]; then
	fi		fi

	# test manual setup		# test manual setup
	bash launch_universc.sh -t "smartseq3" --setup		bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt"

	if [[ -d input4cellranger_test-smartseq3 ]]; then		if [[ -d input4cellranger_test-smartseq3 ]]; then
	rm -rf input4cellranger_test-smartseq3		rm -rf input4cellranger_test-smartseq3
	@@ -44,5 +44,5 @@ bash launch_universc.sh --id "test-smartseq3" --technology "smartseq3" \
	--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
	--read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \		--read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \
	--read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \		--read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \
	--barcodefile "${whitelistdir}/SmartSeq3_test_barcodes.txt" \		--barcodefile "${whitelistdir}/test_bcs_small.txt" \
	--jobmode "local" --localcores 1		--jobmode "local" --localcores 1

test/run_tests_smartseq3_local.sh

+242 −21

Original line number	Original line	Diff line number	Diff line

	#!/bin/bash		#!/bin/bash
			bash ~/.bashrc

	# run tests in universc directory (parent of test directory)		# run tests in universc directory (parent of test directory)
	cd $(dirname ${BASH_SOURCE[0]})/..		cd $(dirname ${BASH_SOURCE[0]})/..
	@@ -20,40 +22,259 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[
	fi		fi

	# compress all input files		# compress all input files
	if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_R1.fastq ]]; then		if [[ -f test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.R1.fastq ]]; then
	gzip test/shared/smartseq3-test/*fastq		echo gzip test/shared/smartseq3-test//Smartseq3.Fibroblasts.GelCut*fastq
	fi		fi

	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.Fibroblasts.GelCut.L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.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.Fibroblasts.GelCut.L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.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.Fibroblasts.GelCut.L001_I1_001.fastq.gz test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.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		#mv test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001_I2_001.fastq.gz test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.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		rename -f "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq
			rename -f "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq

			#rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g" test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.[IR][12].fastq
			#rename "s/Smartseq3.Fibroblasts.GelCut./Smartseq3_Fibroblasts_GelCut_/g" test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.L001.[IR][12].fastq

	# test manual setup		# test manual setup
	bash launch_universc.sh -t "smartseq3" --setup		bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt"

	if [[ -d input4cellranger_test-smartseq3 ]]; then		if [[ false ]]; then
	rm -rf input4cellranger_test-smartseq3
			if [[ -d input4cellranger_test-smartseq3-gelcut-small-hard ]]; then
			rm -rf input4cellranger_test-smartseq3-gelcut-small-hard
	fi		fi
	if [[ -d test-smartseq3 ]]; then		if [[ -d test-smartseq3-gelcut-small-hard ]]; then
	rm -rf test-smartseq3		rm -rf test-smartseq3-gelcut-small-hard
	fi		fi

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


			skip="false"
			#while [[ ! -f /home/tom/repos/universc/test-smartseq3-gelcut/outs/metrics_summary.csv ]]; do
			# echo "wait ..."
			# sleep 60
			#done

			#gzip -fk test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_[IR][12].fastq

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr2-hg38" --technology "smartseq3" \
			--chemistry "SC5P-R2" \
			--reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*
			fi

			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr1-hg38" --technology "smartseq3" \
			--chemistry "SC5P-R1" \
			--reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-hg38" --technology "smartseq3" \
			--chemistry "SC5P-PE" \
			--reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr2" --technology "smartseq3" \
			--chemistry "SC5P-R2" \
			--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard-5pr1" --technology "smartseq3" \
			--chemistry "SC5P-R1" \
			--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hard" --technology "smartseq3" \
			--chemistry "SC5P-PE" \
			--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_hard_[IR][12]_001.fastq*
			fi

			#exit 0

			if [[ -d input4cellranger_test-smartseq3-gelcut-small ]]; then
			rm -rf input4cellranger_test-smartseq3-gelcut-small
			fi
			if [[ -d test-smartseq3-gelcut-small ]]; then
			rm -rf test-smartseq3-gelcut-small
			fi


			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr2-hg38" --technology "smartseq3" \
			--chemistry "SC5P-R2" \
			--reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1

			# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*
			fi

	# call on smartseq3 with files		# call on smartseq3 with files
	bash launch_universc.sh --id "test-smartseq3" --technology "smartseq3" \		bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr1-hg38" --technology "smartseq3" \
			--chemistry "SC5P-R1" \
			--reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1

			# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-hg38" --technology "smartseq3" \
			--chemistry "SC5P-PE" \
			--reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1

			# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr2" --technology "smartseq3" \
			--chemistry "SC5P-R2" \
	--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \		--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
	--read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \		--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \
	--read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \		--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \
	--barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \		--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \
	--per-cell-data --jobmode "local" --localcores 1		--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1

	if [ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz ]; then		# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \
	rename "s/_S1_L001/_S1/" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq*
	rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_[IR][12]_001.fastq*		if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*
	fi		fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small-5pr1" --technology "smartseq3" \
			--chemistry "SC5P-R1" \
			--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1

			# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*
			fi

			# call on smartseq3 with files
			bash launch_universc.sh --id "test-smartseq3-gelcut-small" --technology "smartseq3" \
			--chemistry "SC5P-PE" \
			--reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
			--read1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R1.fastq" \
			--read2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_R2.fastq" \
			--index1 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I1.fastq" \
			--index2 "test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_I2.fastq" \
			--barcodefile "whitelists/Smartseq3_Fibroblasts_GelCut_small_bcs.txt" \
			--per-cell-data --jobmode "sge" #--as-is # "local" --localcores 1

			# --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \

			if [ -f test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_R1_001.fastq ]; then
			rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_S1_L001_[IR][12]_001.fastq*
			rename "s/_001//" test/shared/smartseq3-test/Smartseq3_Fibroblasts_GelCut_small_[IR][12]_001.fastq*
			fi

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