plasmid-assembly/.github/workflows/tests.yml at 26498aa1af72f12c2564dac973835b0094721b59 · BCCDC-PHL/plasmid-assembly · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
on:
  pull_request:
    branches:
      - main
  push:
    branches:
      - main
  workflow_dispatch:
name: Tests
jobs:
  test:
    strategy:
      fail-fast: false
      matrix:
        nextflow_version: ["21.04.3", "23.10.1"]
    name: Run tests
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@master
    - name: Create Artifacts Directory
      run: mkdir artifacts
    - name: Setup Java
      uses: actions/setup-java@v4
      with:
        java-version: '11'
        distribution: 'temurin'
        architecture: x64
    - name: Install Miniconda
      run: bash .github/scripts/install_conda.sh
    - name: Install Nextflow
      env:
        NXF_VER: ${{ matrix.nextflow_version }}
      run: bash .github/scripts/install_nextflow.sh
    - name: Create ART Short Read Simulation Environment
      run: bash .github/scripts/create_art_environment.sh
    - name: Create Badread Long Read Simulation Environment
      run: bash .github/scripts/create_badread_environment.sh
    - name: Download Assemblies
      run: bash .github/scripts/download_assemblies.sh
    - name: Simulate Short Reads
      run: bash .github/scripts/simulate_short_reads.sh
    - name: Simulate Long Reads
      run: bash .github/scripts/simulate_long_reads.sh
    - name: Create plassembler environment
      run: bash .github/scripts/create_plassembler_environment.sh
    - name: Create plassembler db
      run: bash .github/scripts/create_plassembler_db.sh
    - name: Run Pipeline
      run: bash .github/scripts/run_pipeline.sh
    - name: Create Output Checking Environment
      run: bash .github/scripts/create_output_checking_environment.sh
    - name: Check Outputs
      run: bash .github/scripts/check_outputs.sh
    - name: Prepare Artifacts
      if: always()
      run: bash .github/scripts/prepare_artifacts.sh
    - name: Upload Artifacts
      uses: actions/upload-artifact@v4
      if: always()
      with:
        name: artifacts-BCCDC-PHL-tbprofiler-nf-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }}
        path: artifacts