STRling/.github/workflows/ci.yml at 42a3b6e6856cac46b0ff7ad19fc529987139667f · quinlan-lab/STRling · GitHub

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name: CI

on:
  push:
    branches: [ master, dev ]
  pull_request:
    branches: [ master, dev ]
  workflow_dispatch:

jobs:
  build-test:
    runs-on: ubuntu-latest
    env:
      NIM_VERSION: 1.6.10
      HTSLIB_VERSION: 1.22.1
    steps:
      - name: Checkout
        uses: actions/checkout@v4

      - name: Cache nimble packages
        uses: actions/cache@v4
        with:
          path: ~/.nimble
          key: nimble-${{ runner.os }}-${{ hashFiles('strling.nimble') }}
          restore-keys: |
            nimble-${{ runner.os }}-

      - name: Setup Nim
        run: |
          export CHOOSENIM_CHOOSE_VERSION=$NIM_VERSION
          curl https://nim-lang.org/choosenim/init.sh -sSf > init.sh
          sh init.sh -y
          echo "$HOME/.nimble/bin" >> $GITHUB_PATH
          export PATH=/home/runner/.nimble/bin:$PATH

      - name: Install system build deps
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential autoconf automake libcurl4-openssl-dev libssl-dev zlib1g-dev libbz2-dev liblzma-dev wget unzip

      - name: Build htslib
        run: |
          wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
          tar xjf htslib-${HTSLIB_VERSION}.tar.bz2
          cd htslib-${HTSLIB_VERSION}
          autoheader && autoconf && ./configure --enable-libcurl
          make -j 2
          echo "LD_LIBRARY_PATH=$PWD" >> $GITHUB_ENV

      - name: Nimble install
        run: nimble install -y

      - name: Build strling help
        run: ./strling -h

      - name: Unit tests
        run: nimble test -y

  integration-e2e:
    # Only run end-to-end tests on pushes to master to keep PRs fast
    if: github.ref == 'refs/heads/master'
    runs-on: ubuntu-latest
    needs: build-test
    env:
      HTSLIB_VERSION: 1.10
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Setup Nim
        run: |
          export CHOOSENIM_CHOOSE_VERSION=$NIM_VERSION
          curl https://nim-lang.org/choosenim/init.sh -sSf > init.sh
          sh init.sh -y
          echo "$HOME/.nimble/bin" >> $GITHUB_PATH
          export PATH=/home/runner/.nimble/bin:$PATH
      - name: Install system build deps
        run: |
          sudo apt-get update
          sudo apt-get install -y build-essential autoconf automake libcurl4-openssl-dev libssl-dev zlib1g-dev libbz2-dev liblzma-dev wget unzip
      - name: Build htslib
        run: |
          wget https://github.com/samtools/htslib/releases/download/${HTSLIB_VERSION}/htslib-${HTSLIB_VERSION}.tar.bz2
          tar xjf htslib-${HTSLIB_VERSION}.tar.bz2
          cd htslib-${HTSLIB_VERSION}
          autoheader && autoconf && ./configure --enable-libcurl
          make -j 2
          echo "LD_LIBRARY_PATH=$PWD" >> $GITHUB_ENV
      - name: Nimble install
        run: nimble install -y
      - name: Download test data
        run: |
          mkdir -p run_tests
          cd run_tests
          wget -O data.zip https://ndownloader.figshare.com/articles/11367851?private_link=207b2a78ddcbdb28781b
          unzip data.zip
          rm data.zip
          wget -O chr4.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr4.fa.gz
          gzip -d chr4.fa.gz
      - name: End-to-end single sample
        run: |
          cd run_tests
          mkdir -p single
          ../strling extract -f chr4.fa -g chr4.fa.str -v CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin
          ../strling call -v -o single/CANVAS.chr4-39348425_AAGGG_0_400 CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin
      - name: End-to-end joint samples
        run: |
          cd run_tests
          mkdir -p joint
          for i in *.bam; do ../strling extract -f chr4.fa -g chr4.fa.str -v $i joint/$i.str.bin; done
          ../strling merge -f chr4.fa -v -o joint/strling joint/*.bin
          for i in *.bam; do ../strling call -v -b joint/strling-bounds.txt -o joint/$i $i joint/$i.str.bin; done
      - name: Inspect outputs
        run: |
          cd run_tests
          head single/*.txt || true
          head joint/strling-bounds.txt || true
          head joint/*.txt || true