Specify 72 GB memory for kraken2 #2
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on: | |
pull_request: | |
branches: | |
- master | |
name: Tests | |
jobs: | |
test: | |
strategy: | |
fail-fast: false | |
matrix: | |
nextflow_version: ["21.04.3", "23.10.1", "24.04.3"] | |
name: Run tests | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@master | |
- name: Create artifacts dir to save test logs | |
run: mkdir -p artifacts | |
- name: Install Conda | |
run: bash .github/scripts/install_conda.sh | |
- name: Install Nextflow | |
env: | |
NXF_VER: ${{ matrix.nextflow_version }} | |
run: bash .github/scripts/install_nextflow.sh | |
- name: Set up conda cache environment | |
run: bash .github/scripts/set_up_conda_cache.sh | |
- name: Download hg38 chr22 | |
run: bash .github/scripts/download_hg38_chr22.sh | |
- name: Create kraken2/bracken db | |
run: bash .github/scripts/create_kraken2_and_bracken_database.sh | |
- name: Run Pipeline | |
env: | |
NXF_VER: ${{ matrix.nextflow_version }} | |
run: bash .github/scripts/test_pipeline.sh | |
- uses: actions/upload-artifact@v1 | |
if: always() | |
with: | |
name: artifacts-BCCDC-PHL-dehost-and-verify-illumina-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }} | |
path: artifacts |