test job for Smart-Seq3

name: Test Smart-Seq3

on: push

jobs:

  test:

    runs-on: ubuntu-20.04

    steps:

      - uses: actions/checkout@v2

      - name: Build the stack

        run: docker-compose up -d

      - name: Status

        run: echo "build complete" 

  test-dropseq:

    runs-on: ubuntu-20.04

    steps:

    - uses: actions/checkout@v2

    - uses: docker/setup-buildx-action@v1

    - uses: docker/login-action@v1

      with:

        username: ${{ secrets.DOCKER_HUB_USERNAME }}

        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

        registry: ${{ env.REGISTRY }}

    - name: Build and push

      uses: docker/build-push-action@v2

      with:

        context: ./

        file: ./Dockerfile

        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest

        push: false

    - name: Test DropSeq

      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_smartseq3_gh_actions.sh

#!/bin/bash

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

cd $(dirname ${BASH_SOURCE[0]})/..

pwd

# used to export to PATH for testing on SGE server

export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH

cellrangerversion=`cellranger count --version | head -n 2 | tail -n 1 | cut -f2 -d'(' | cut -f1 -d')'`

cellrangerpath=`which cellranger`

# set up cellranger reference

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then

    ln $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA

fi

if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then

    ln $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA

fi

rm -rf test/shared/smartseq3-test/* test/shared/cellranger-tiny-fastq/* test/shared/mappa-test/

rm -rf  test/cellranger_reference/cellranger-tiny-ref/1.2.0

# compress all input files

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

    gzip test/shared/smartseq3-test/*fastq

fi

# reset test data (compress)

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

   gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq

fi

if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq ]]; then

    gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq

fi

# reset test data (files names)

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz

fi

## test drop-seq data

# unzip input data

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

    unpigz -f test/shared/smartseq3-test/*fastq.gz

fi

# test manual setup

bash launch_universc.sh -t "smartseq" --setup

# remove processed files

if [[ -f SRR1873277_S1_L001_R[12]_001.fastq ]]; then

    rm SRR1873277_S1_L001_R[12]_001.fastq

fi

if [[ -d input4cellranger_test-smartseq3 ]]; then

    rm -rf input4cellranger_test-smartseq3

fi

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

    rm -rf test-smartseq3

fi

# call on smartseq3 with files

bash launch_universc.sh --id "test-smartseq3" --technology "smartseq" \

 --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" \

 --jobmode "local" --localcores 1 

# reset test data (compress)

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

   gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq

fi

if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq ]]; then

    gzip -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq

fi

# reset test data (files names)

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz

fi

if [[ ! -f test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz ]]; then

    mv test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz

else

    rm test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq.gz

fi

# compress all input files

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

    gzip test/shared/smartseq3-test/*fastq

fi