Add nf-test sharding CI #6263
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name: nf-core CI | |
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
on: | |
push: | |
branches: | |
- dev | |
pull_request: | |
release: | |
types: [published] | |
env: | |
NXF_ANSI_LOG: false | |
NFT_VER: "0.9.0" | |
NFT_WORKDIR: "~" | |
NFT_DIFF: "pdiff" | |
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | |
TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
name: ${{ matrix.NXF_VER }} | ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }} | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: ["23.04.0", "latest-everything"] # TODO Test minimum version on release | |
filter: ["pipeline", "workflow"] # TODO Modules and Functions | |
profile: ["docker"] | |
shard: [1, 2, 3, 4, 5] | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
fetch-depth: 0 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
architecture: "x64" | |
- name: Install pdiff to see diff between nf-test snapshots | |
run: | | |
python -m pip install --upgrade pip | |
pip install pdiff | |
- uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- uses: nf-core/setup-nf-test@v1 | |
with: | |
version: ${{ env.NFT_VER }} | |
- name: Set up miniconda | |
if: matrix.profile == 'conda' | |
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
with: | |
miniconda-version: "latest" | |
auto-update-conda: true | |
channels: conda-forge,bioconda,defaults | |
- name: Conda setup | |
if: matrix.profile == 'conda' | |
run: | | |
conda clean -a | |
conda install -n base conda-libmamba-solver | |
conda config --set solver libmamba | |
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
echo $(realpath python) >> $GITHUB_PATH | |
- name: Set up nextflow secrets | |
if: env.SENTIEON_LICENSE_BASE64 != null | |
run: | | |
nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }} | |
SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d) | |
SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
SENTIEON_AUTH_DATA=$(python3 bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | |
nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | |
- name: Disk space cleanup | |
uses: jlumbroso/[email protected] | |
- name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) | |
run: | | |
nf-test test \ | |
--ci \ | |
--junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \ | |
--verbose \ | |
--shard ${{ matrix.shard }}/5 \ | |
--changed-since HEAD^ \ | |
--profile "+${{ matrix.profile }}" \ | |
--filter ${{ matrix.filter }} | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v4 | |
if: success() || failure() # always run even if the previous step fails | |
with: | |
report_paths: "TEST-*.xml" | |
- name: Clean up | |
if: always() | |
run: | | |
sudo rm -rf /home/ubuntu/tests/ |