Commit e59e78c4 authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update test data for SmartSeq3 from published data 

updates test data files (imported from published data)
updates test jobs and GH Actions
parent 7b258f20

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

+1 −0
Original line number Diff line number Diff line 




name: Run all tests in Docker

on: push

jobs:

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

+4 −4
Original line number Diff line number Diff line 
name: Test Smart-Seq3

name: Test ICELL8

on: push

jobs:

  test:
@@ -10,7 +10,7 @@ jobs: 
      - name: Status

        run: echo "build complete" 



  test-smart-seq3:

  test-smartseq3:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2
@@ -30,5 +30,5 @@ jobs: 
        push: false

    - name: clear environment

      run: rm -rf *

    - name: Test Smart-Seq3

      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
 
    - name: Test ICELL8

      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

+3 −0
Original line number Diff line number Diff line
@@ -18,6 +18,9 @@ PYTHON_SITE_PKG:=$(lastword $(wildcard $(PYTHON_LIB_DIR)/python*/site-packages)) 
PYTHON_CFLAGS:=$(shell python-config --cflags)

PYTHON_LDFLAGS:=$(shell python-config --ldflags)



test-data:

	make -C test/shared/smartseq3-test



reference:

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

test/run_tests_smartseq3_gh_actions.sh

+2 −2
Original line number Diff line number Diff line
@@ -26,7 +26,7 @@ if [[ -f test/shared/smartseq3-test/*fastq ]]; then 
fi



# 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

    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" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \

 --barcodefile "${whitelistdir}/SmartSeq3_test_barcodes.txt" \

 --barcodefile "${whitelistdir}/test_bcs_small.txt" \

 --jobmode "local" --localcores 1

test/run_tests_smartseq3_local.sh

+242 −21
Original line number Diff line number Diff line 


#!/bin/bash

bash ~/.bashrc



# run tests in universc directory (parent of test directory)

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



# compress all input files

if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_R1.fastq ]]; then

    gzip test/shared/smartseq3-test/*fastq

if [[ -f test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.R1.fastq ]]; then

echo    gzip test/shared/smartseq3-test//Smartseq3.Fibroblasts.GelCut*fastq

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_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

#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.Fibroblasts.GelCut.L001_R2_001.fastq.gz  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.R2.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.Fibroblasts.GelCut.L001_I2_001.fastq.gz  test/shared/smartseq3-test/Smartseq3.Fibroblasts.GelCut.I2.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

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

    rm -rf input4cellranger_test-smartseq3

if [[ false ]]; then



if [[ -d input4cellranger_test-smartseq3-gelcut-small-hard ]]; then

    rm -rf input4cellranger_test-smartseq3-gelcut-small-hard

fi

if [[ -d test-smartseq3 ]]; then

    rm -rf test-smartseq3

if [[ -d test-smartseq3-gelcut-small-hard ]]; then

    rm -rf test-smartseq3-gelcut-small-hard

fi



if [[ ! -f whitelists/SmartSeq3_test_barcodes.txt ]]; then

    gunzip -k whitelists/SmartSeq3_test_barcodes.txt.gz

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

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" \

 --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_R1" \

 --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_R2" \

 --barcodefile "whitelists/SmartSeq3_test_barcodes.txt" \

 --per-cell-data --jobmode "local" --localcores 1

 --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



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

    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*

# --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-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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