CI: add gpu tag test job #1085
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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] | |
workflow_dispatch: | |
env: | |
NXF_ANSI_LOG: false | |
NFT_VER: "0.9.2" | |
NFT_WORKDIR: "~" | |
NFT_DIFF: "pdiff" | |
NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
nf-test-gpu: | |
name: "Run GPU Tests (${{ matrix.NXF_VER }} | ${{ matrix.profile }})" | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | |
runs-on: "gpu" | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
shard: [1, 2] | |
filter: [pipeline, workflow] | |
profile: | |
- "docker" | |
- "singularity" | |
isMaster: | |
- ${{ github.base_ref == 'master' }} | |
# Exclude singularity on dev | |
exclude: | |
- isMaster: false | |
profile: "singularity" | |
env: | |
NXF_ANSI_LOG: false | |
TOTAL_SHARDS: 2 | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
fetch-depth: 0 | |
- name: Set up Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Set up Python | |
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | |
with: | |
python-version: "3.11" | |
- name: Install nf-test | |
uses: nf-core/setup-nf-test@v1 | |
with: | |
version: "${{ env.NFT_VER }}" | |
install-pdiff: true | |
- name: Set up Apptainer | |
if: matrix.profile == 'singularity' | |
uses: eWaterCycle/setup-apptainer@main | |
- name: Set up Singularity | |
if: matrix.profile == 'singularity' | |
run: | | |
mkdir -p $NXF_SINGULARITY_CACHEDIR | |
mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
# Set up secrets | |
- name: Set up nextflow secrets | |
if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != '' | |
shell: bash | |
run: | | |
python -m pip install cryptography | |
nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | |
# TODO Skip failing conda tests and document their failures | |
# https://github.com/nf-core/modules/issues/7017 | |
- name: Clean up Disk space | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Run GPU Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}) | |
run: | | |
nf-test test \ | |
--ci \ | |
--shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ | |
--changed-since HEAD^ \ | |
--profile "+${{ matrix.profile }}" \ | |
--filter ${{ matrix.filter }} \ | |
--tag "gpu" | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/**/nextflow.log | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v3 | |
if: always() # always run even if the previous step fails | |
with: | |
report_paths: test.xml | |
nf-test: | |
name: "Run CPU Tests (${{ matrix.NXF_VER }} | ${{ matrix.profile }})" | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "24.04.2" | |
- "latest-everything" | |
shard: [1, 2] | |
filter: [pipeline, workflow] | |
profile: | |
- "conda" | |
- "docker" | |
- "singularity" | |
isMaster: | |
- ${{ github.base_ref == 'master' }} | |
# Exclude conda and singularity on dev | |
exclude: | |
- isMaster: false | |
profile: "conda" | |
- isMaster: false | |
profile: "singularity" | |
env: | |
NXF_ANSI_LOG: false | |
TOTAL_SHARDS: 2 | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | |
with: | |
fetch-depth: 0 | |
- name: Set up Nextflow | |
uses: nf-core/setup-nextflow@v2 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Install pdiff to see diff between nf-test snapshots | |
run: | | |
python -m pip install --upgrade pip | |
pip install pdiff | |
- uses: nf-core/setup-nf-test@v1 | |
with: | |
version: ${{ env.NFT_VER }} | |
- name: Set up Apptainer | |
if: matrix.profile == 'singularity' | |
uses: eWaterCycle/setup-apptainer@main | |
- name: Set up Singularity | |
if: matrix.profile == 'singularity' | |
run: | | |
mkdir -p $NXF_SINGULARITY_CACHEDIR | |
mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
- name: Set up Miniconda | |
if: matrix.profile == 'conda' | |
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
with: | |
miniconda-version: "latest" | |
auto-update-conda: true | |
conda-solver: libmamba | |
channels: conda-forge,bioconda | |
- name: Set up Conda | |
if: matrix.profile == 'conda' | |
run: | | |
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
echo $(realpath python) >> $GITHUB_PATH | |
- name: Clean up Disk space | |
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | |
- name: Run Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}) | |
run: | | |
nf-test test \ | |
--ci \ | |
--shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ | |
--changed-since HEAD^ \ | |
--profile "+${{ matrix.profile }}" \ | |
--filter ${{ matrix.filter }} \ | |
--tag "cpu" | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
- name: Publish Test Report | |
uses: mikepenz/action-junit-report@v3 | |
if: always() # always run even if the previous step fails | |
with: | |
report_paths: test.xml |