1357 grouping strategy applied by counting number of FASTQ files generated by FASTP #5455
Workflow file for this run
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name: test | |
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
on: | |
pull_request: | |
release: | |
types: [published] | |
merge_group: | |
types: | |
- checks_requested | |
branches: | |
- master | |
- dev | |
env: | |
NXF_ANSI_LOG: false | |
NFTEST_VER: "0.8.1" | |
# Cancel if a newer run is started | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
jobs: | |
pytest-changes: | |
name: Check for changes (pytest) | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'tags' output variable | |
tags: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: frouioui/paths-filter@main | |
id: filter | |
with: | |
filters: "tests/config/pytesttags.yml" | |
token: "" | |
pytest: | |
name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
runs-on: ubuntu-latest | |
needs: pytest-changes | |
if: needs.pytest-changes.outputs.tags != '[]' | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: ["${{ fromJson(needs.pytest-changes.outputs.tags) }}"] | |
profile: ["docker"] | |
# profile: ["docker", "singularity", "conda"] | |
TEST_DATA_BASE: | |
- "test-datasets/data" | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
env: | |
NXF_ANSI_LOG: false | |
TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v4 | |
- name: Hash Github Workspace | |
id: hash_workspace | |
run: | | |
echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: "3.x" | |
cache: "pip" | |
cache-dependency-path: | | |
**/requirements.txt | |
- name: Install Python dependencies | |
run: pip install --upgrade -r tests/requirements.txt | |
- name: Install Nextflow ${{ matrix.NXF_VER }} | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Set up Singularity | |
if: matrix.profile == 'singularity' | |
uses: eWaterCycle/setup-singularity@v5 | |
with: | |
singularity-version: 3.7.1 | |
- name: Set up miniconda | |
if: matrix.profile == 'conda' | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
auto-update-conda: true | |
channels: conda-forge,bioconda,defaults | |
python-version: ${{ matrix.python-version }} | |
- name: Cache test data | |
id: cache-testdata | |
uses: actions/cache@v3 | |
with: | |
path: test-datasets/ | |
key: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v4 | |
with: | |
repository: nf-core/test-datasets | |
ref: sarek3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in tests/csv/3.0/*csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
# Set up secrets | |
- 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 "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d) | |
SENTIEON_AUTH_DATA=$(python 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 $SENTIEON_AUTH_DATA_BASE64 | |
- name: Conda clean | |
if: matrix.profile == 'conda' | |
run: conda clean -a | |
- name: Run pytest-workflow | |
uses: Wandalen/wretry.action@v1 | |
with: | |
command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
attempt_limit: 3 | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
- name: Upload logs on failure | |
if: failure() | |
uses: actions/upload-artifact@v2 | |
with: | |
name: logs-${{ matrix.profile }} | |
path: | | |
/home/runner/pytest_workflow_*/*/.nextflow.log | |
/home/runner/pytest_workflow_*/*/log.out | |
/home/runner/pytest_workflow_*/*/log.err | |
/home/runner/pytest_workflow_*/*/work | |
!/home/runner/pytest_workflow_*/*/work/conda | |
!/home/runner/pytest_workflow_*/*/work/singularity | |
nftest-changes: | |
name: Check for changes (nf-test) | |
runs-on: ubuntu-latest | |
outputs: | |
tags: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Combine all tags.yml files | |
id: get_tags | |
run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
- name: debug | |
run: cat .github/tags.yml | |
- uses: frouioui/paths-filter@main | |
id: filter | |
with: | |
filters: ".github/tags.yml" | |
token: "" | |
nftest: | |
name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }} | |
runs-on: ubuntu-latest | |
needs: nftest-changes | |
if: needs.nftest-changes.outputs.tags != '[]' | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: ["${{ fromJson(needs.nftest-changes.outputs.tags) }}"] | |
profile: ["docker"] | |
# profile: ["docker", "singularity", "conda"] | |
TEST_DATA_BASE: | |
- "test-datasets/data" | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
exclude: | |
- tags: "bwa/index" | |
- tags: "bwa/mem" | |
- tags: "cat/cat" | |
- tags: "cat/fastq" | |
- tags: "custom/dumpsoftwareversions" | |
- tags: "dragmap/align" | |
- tags: "fastp" | |
- tags: "fastqc" | |
- tags: "multiqc" | |
- tags: "samtools/stats" | |
- tags: "untar" | |
env: | |
NXF_ANSI_LOG: false | |
TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-java@v3 | |
with: | |
distribution: "temurin" | |
java-version: "17" | |
- name: Setup Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
- name: Cache nf-test installation | |
id: cache-software | |
uses: actions/cache@v3 | |
with: | |
path: | | |
/usr/local/bin/nf-test | |
/home/runner/.nf-test/nf-test.jar | |
key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest | |
- name: Install nf-test | |
if: steps.cache-software.outputs.cache-hit != 'true' | |
run: | | |
wget -qO- https://code.askimed.com/install/nf-test | bash | |
sudo mv nf-test /usr/local/bin/ | |
- name: Setup 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 | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: "latest" | |
auto-update-conda: true | |
channels: conda-forge,bioconda,defaults | |
python-version: ${{ matrix.python-version }} | |
- name: Conda setup | |
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 | |
# Set up secrets | |
- 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 $SENTIEON_AUTH_DATA_BASE64 | |
# Test the module | |
- name: Run nf-test | |
run: | | |
nf-test test \ | |
--profile=${{ matrix.profile }} \ | |
--tag ${{ matrix.tags }} \ | |
--tap=test.tap \ | |
--verbose | |
confirm-pass: | |
runs-on: ubuntu-latest | |
needs: | |
- pytest | |
- nftest | |
if: always() | |
steps: | |
- name: All tests ok | |
if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
run: exit 0 | |
- name: One or more tests failed | |
if: ${{ contains(needs.*.result, 'failure') }} | |
run: exit 1 | |
- name: debug-print | |
if: always() | |
run: | | |
echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |