.gitlab-ci.yml

# use a debian-based image.
image: ubuntu:bionic

before_script:
   - apt update && apt -y install g++ make autoconf automake 
     libtool gnulib gengetopt zlib1g-dev libboost-dev libboost-filesystem-dev 
     libboost-system-dev libboost-iostreams-dev libboost-test-dev 
     libbamtools-dev

build:
  stage: build
  script:
    - autoreconf -fi
    - ./configure --enable-tests --prefix="$(pwd)/install-${CI_COMMIT_SHORT_SHA}"
    - make -j
    - make install
    - cd tests; make check -j;
  artifacts:
    paths:
      - install-${CI_COMMIT_SHORT_SHA}/bin/idemuxCPP
      - install-${CI_COMMIT_SHORT_SHA}/share/idemuxcpp/

unit-tests:
  stage: test
  needs: ["build"]
  script:
    - printf "================\n Run Unit Tests \n================\n"
    - apt update && apt install -y lcov
    - autoreconf -fi
    - ./configure --enable-code-coverage
    - make check-code-coverage -j
  coverage:
    '/^\s*lines\.*\:\s*(\d*\.?\d*\%)/'

# run integration tests
test_integration:
  stage: test
  needs: ["build"]
  script:
    - export INSTALL_DIR="$(pwd)/install-${CI_COMMIT_SHORT_SHA}"
    - tmpread1=`mktemp`
    - echo -e "@header1 :AAAAACGGCAGG+AAAAGTTATTCT\nAAAAGTTATTCT\n+\nEEEEEEEEEEEE\n"\
              "@header2 :AAAACATGCGTT+AAACAAGTCCGA\nAAACAAGTCCGA\n+\nEEEEEEEEEEEE\n"\
              "@header3 :AAAATCCCAGTT+AAACCTTTTGAA\nAAACCTTTTGAA\n+\nEEEEEEEEEEEE\n"\
              "@header4 :AAAAAAAAAAAA+AAAAAAAAAAAA\nAAAAAAAAAAAA\n+\nEEEEEEEEEEEE"\
      | gzip - > ${tmpread1}.fastq.gz
    - tmpsdf=`mktemp`
    - echo -e "sample_name,i7,i5,i1\n"\
              "1,AAAAACGGCAGG,AAAAGTTATTCT,\n"\
              "2,AAAACATGCGTT,AAACAAGTCCGA,\n"\
              "3,AAAATCCCAGTT,AAACCTTTTGAA,"\
      > ${tmpsdf}
    - tmpoutput=`mktemp -d`
    - ${INSTALL_DIR}/bin/idemuxCPP -1 ${tmpread1}.fastq.gz -s ${tmpsdf} -o ${tmpoutput} -m "${INSTALL_DIR}/share/idemuxcpp/barcodes/"
    - cat ${tmpoutput}/demultipexing_stats.tsv | sort > ${tmpoutput}/a.txt
    - echo -e "1\t1\n2\t1\n3\t1\nsample_name\twritten_reads\nundetermined\t1" > ${tmpoutput}/b.txt
    - diff ${tmpoutput/}/a.txt ${tmpoutput}/b.txt
    - echo $?