This repository has been archived by the owner on May 2, 2024. It is now read-only.
nf-test for module PROKKA (#4602) #6
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name: Run tests | |
on: | |
push: | |
branches: [master] | |
pull_request: | |
branches: [master] | |
merge_group: | |
types: [checks_requested] | |
branches: [master] | |
# Cancel if a newer run is started | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
env: | |
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
jobs: | |
pre-commit: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: actions/setup-python@v3 | |
- uses: pre-commit/[email protected] | |
# FIXME Flip this off once we get to less than a couple hundred. Adding | |
# this so it will only run against changed files. It'll make it much | |
# easier to fix these as they come up rather than everything at once. | |
with: | |
extra_args: "" | |
prettier: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Check out repository | |
uses: actions/checkout@v4 | |
- name: Install NodeJS | |
uses: actions/setup-node@v4 | |
with: | |
node-version: "20" | |
- name: Install Prettier | |
run: npm install -g prettier | |
- name: Run Prettier --check | |
run: prettier --check . | |
editorconfig: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-node@v4 | |
with: | |
node-version: "20" | |
- name: Install editorconfig-checker | |
run: npm install -g editorconfig-checker | |
- name: Run ECLint check | |
run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
pytest-changes: | |
name: pytest-changes | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'modules' output variable | |
modules: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 # To retrieve the preceding commit. | |
# TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
- uses: mirpedrol/paths-filter@main | |
id: filter | |
with: | |
filters: "tests/config/pytest_modules.yml" | |
token: "" | |
nf-test-changes: | |
name: nf-test-changes | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'modules' output variable | |
modules: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 2 # To retrieve the preceding commit. | |
- 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 | |
# TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
- uses: mirpedrol/paths-filter@main | |
id: filter | |
with: | |
filters: ".github/tags.yml" | |
token: "" | |
nf-core-lint: | |
runs-on: ubuntu-latest | |
name: nf-core-lint | |
needs: [pytest-changes, nf-test-changes] | |
if: ${{ (needs.pytest-changes.outputs.modules != '[]') || (needs.nf-test-changes.outputs.modules != '[]') }} | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: | |
[ | |
"${{ fromJson(needs.pytest-changes.outputs.modules) }}", | |
"${{ fromJson(needs.nf-test-changes.outputs.modules) }}", | |
] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
- uses: actions/cache@v3 | |
with: | |
path: ~/.cache/pip | |
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
restore-keys: | | |
${{ runner.os }}-pip- | |
- name: Install pip | |
run: python -m pip install --upgrade pip | |
- uses: actions/setup-java@v3 | |
with: | |
distribution: "temurin" | |
java-version: "17" | |
- name: Setup Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
- name: Install nf-core tools development version | |
run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
- name: Lint module ${{ matrix.tags }} | |
run: nf-core modules lint ${{ matrix.tags }} | |
if: ${{ !startsWith(matrix.tags, 'subworkflows/') }} | |
- name: Remove substring from matrix.tags | |
id: remove_substring | |
run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT | |
- name: Lint subworkflow ${{ matrix.tags }} | |
run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}} | |
if: ${{ startsWith(matrix.tags, 'subworkflows/') }} | |
pytest: | |
runs-on: ubuntu-latest | |
name: pytest | |
needs: [pytest-changes] | |
if: needs.pytest-changes.outputs.modules != '[]' | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: ["${{ fromJson(needs.pytest-changes.outputs.modules) }}"] | |
profile: ["docker", "singularity", "conda"] | |
exclude: | |
- tags: "nf-test" | |
- profile: "conda" | |
tags: annotsv | |
- profile: "conda" | |
tags: happy/sompy | |
- profile: "conda" | |
tags: cellpose | |
- profile: "conda" | |
tags: mcquant | |
- profile: "conda" | |
tags: bases2fastq | |
- profile: "conda" | |
tags: backsub | |
- profile: "conda" | |
tags: basicpy | |
- profile: "conda" | |
tags: bcl2fastq | |
- profile: "conda" | |
tags: bclconvert | |
- profile: "conda" | |
tags: bwa/aln | |
- profile: "conda" | |
tags: bwa/index | |
- profile: "conda" | |
tags: bwa/mem | |
- profile: "conda" | |
tags: bwa/sampe | |
- profile: "conda" | |
tags: bwa/samse | |
- profile: "conda" | |
tags: cellranger/count | |
- profile: "conda" | |
tags: cellranger/mkfastq | |
- profile: "conda" | |
tags: cellranger/mkgtf | |
- profile: "conda" | |
tags: cellranger/mkref | |
- profile: "conda" | |
tags: cellranger/mkvdjref | |
- profile: "conda" | |
tags: cellranger/multi | |
- profile: "conda" | |
tags: cellranger/vdj | |
- profile: "conda" | |
tags: checkm2/databasedownload | |
- profile: "conda" | |
tags: checkm2/predict | |
- profile: "conda" | |
tags: cellrangeratac/count | |
- profile: "conda" | |
tags: cellrangeratac/mkfastq | |
- profile: "conda" | |
tags: cellrangeratac/mkref | |
- profile: "conda" | |
tags: controlfreec/makegraph2 | |
- profile: "conda" | |
tags: coreograph | |
- profile: "conda" | |
tags: deepcell/mesmer | |
- profile: "conda" | |
tags: deepvariant | |
- profile: "conda" | |
tags: fastk/fastk | |
- profile: "conda" | |
tags: fastani | |
- profile: "conda" | |
tags: fastk/histex | |
- profile: "conda" | |
tags: fastk/merge | |
- profile: "conda" | |
tags: fcs/fcsadaptor | |
- profile: "conda" | |
tags: fcs/fcsgx | |
- profile: "conda" | |
tags: gatk4/cnnscorevariants | |
- profile: "conda" | |
tags: gatk4/determinegermlinecontigploidy | |
- profile: "conda" | |
tags: gatk4/germlinecnvcaller | |
- profile: "conda" | |
tags: gatk4/postprocessgermlinecnvcalls | |
- profile: "conda" | |
tags: genescopefk | |
- profile: "conda" | |
tags: hlala/preparegraph | |
- profile: "conda" | |
tags: ilastik/multicut | |
- profile: "conda" | |
tags: ilastik/pixelclassification | |
- profile: "conda" | |
tags: imputeme/vcftoprs | |
- profile: "conda" | |
tags: manta/convertinversion | |
- profile: "conda" | |
tags: medaka | |
- profile: "conda" | |
tags: merquryfk/katcomp | |
- profile: "conda" | |
tags: merquryfk/katgc | |
- profile: "conda" | |
tags: merquryfk/merquryfk | |
- profile: "conda" | |
tags: merquryfk/ploidyplot | |
- profile: "conda" | |
tags: minimap2/align | |
- profile: "conda" | |
tags: mitohifi/mitohifi | |
- profile: "conda" | |
tags: mitohifi/findmitoreference | |
- profile: "conda" | |
tags: nanoplot | |
- profile: "conda" | |
tags: ncbitools/vecscreen | |
- profile: "conda" | |
tags: parabricks/applybqsr | |
- profile: "conda" | |
tags: parabricks/deepvariant | |
- profile: "conda" | |
tags: parabricks/fq2bam | |
- profile: "conda" | |
tags: parabricks/haplotypecaller | |
- profile: "conda" | |
tags: parabricks/mutectcaller | |
- profile: "conda" | |
tags: parabricks/indexgvcf | |
- profile: "conda" | |
tags: picard/collecthsmetrics | |
- profile: "conda" | |
tags: picard/collectwgsmetrics | |
- profile: "conda" | |
tags: scimap/mcmicro | |
- profile: "conda" | |
tags: sentieon/applyvarcal | |
- profile: "conda" | |
tags: sentieon/bwaindex | |
- profile: "conda" | |
tags: sentieon/bwamem | |
- profile: "conda" | |
tags: sentieon/datametrics | |
- profile: "conda" | |
tags: sentieon/dedup | |
- profile: "conda" | |
tags: sentieon/dnamodelapply | |
- profile: "conda" | |
tags: sentieon/dnascope | |
- profile: "conda" | |
tags: sentieon/gvcftyper | |
- profile: "conda" | |
tags: sentieon/haplotyper | |
- profile: "conda" | |
tags: sentieon/readwriter | |
- profile: "conda" | |
tags: sentieon/tnfilter | |
- profile: "conda" | |
tags: sentieon/tnhaplotyper2 | |
- profile: "conda" | |
tags: sentieon/tnscope | |
- profile: "conda" | |
tags: sentieon/varcal | |
- profile: "conda" | |
tags: sentieon/wgsmetrics | |
- profile: "conda" | |
tags: spaceranger/count | |
- profile: "conda" | |
tags: spaceranger/mkgtf | |
- profile: "conda" | |
tags: spaceranger/mkref | |
- profile: "conda" | |
tags: svanalyzer/svbenchmark | |
- profile: "conda" | |
tags: universc | |
- profile: "singularity" | |
tags: universc | |
- profile: "conda" | |
tags: vt/decompose | |
- profile: "singularity" | |
tags: gatk4/determinegermlinecontigploidy | |
- profile: "conda" | |
tags: subworkflows/bcl_demultiplex | |
- profile: "conda" | |
tags: subworkflows/fasta_clean_fcs | |
- profile: "conda" | |
tags: islandpath | |
- profile: "conda" | |
tags: subworkflows/bam_qc_picard | |
env: | |
NXF_ANSI_LOG: false | |
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: "3.11" | |
- name: Install Python dependencies | |
run: python -m pip install --upgrade pip pytest-workflow cryptography | |
- uses: actions/setup-java@v3 | |
with: | |
distribution: "temurin" | |
java-version: "17" | |
- name: Setup Nextflow ${{ matrix.NXF_VER }} | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- 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" | |
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 tests/modules/nf-core/sentieon/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 $SENTIEON_AUTH_DATA_BASE64 | |
# Test the module | |
- name: Run pytest-workflow | |
# only use one thread for pytest-workflow to avoid race condition on conda cache. | |
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt-get update > /dev/null | |
sudo apt-get install bat > /dev/null | |
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
- name: Setting global variables | |
uses: actions/github-script@v6 | |
id: parsed | |
with: | |
script: | | |
return '${{ matrix.tags }}'.toLowerCase().replaceAll(/\//g, '-').trim('-').trim('"') | |
result-encoding: string | |
- name: Upload logs on failure | |
if: failure() | |
uses: actions/upload-artifact@v3 | |
with: | |
name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} | |
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 | |
!${{ github.workspace }}/.singularity | |
nf-test: | |
runs-on: ubuntu-latest | |
name: nf-test | |
needs: [nf-test-changes] | |
if: needs.nf-test-changes.outputs.modules != '[]' | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
profile: ["docker", "singularity", "conda"] | |
exclude: | |
- tags: "nf-test" | |
- profile: "conda" | |
tags: annotsv | |
- profile: "conda" | |
tags: happy/sompy | |
- profile: "conda" | |
tags: backsub | |
- profile: "conda" | |
tags: bases2fastq | |
- profile: "conda" | |
tags: bcl2fastq | |
- profile: "conda" | |
tags: bclconvert | |
- profile: "conda" | |
tags: cellranger/count | |
- profile: "conda" | |
tags: cellranger/mkfastq | |
- profile: "conda" | |
tags: cellranger/mkgtf | |
- profile: "conda" | |
tags: cellranger/mkref | |
- profile: "conda" | |
tags: custom/dumpsoftwareversions | |
- profile: "conda" | |
tags: deepcell/mesmer | |
- profile: "conda" | |
tags: deepvariant | |
- profile: "conda" | |
tags: ensemblvep/vep | |
- profile: "conda" | |
tags: fastk/fastk | |
- profile: "conda" | |
tags: fastk/histex | |
- profile: "conda" | |
tags: fastk/merge | |
- profile: "conda" | |
tags: fcs/fcsadaptor | |
- profile: "conda" | |
tags: fcs/fcsgx | |
- profile: "conda" | |
tags: gatk4/cnnscorevariants | |
- profile: "conda" | |
tags: gatk4/determinegermlinecontigploidy | |
- profile: "conda" | |
tags: genescopefk | |
- profile: "conda" | |
tags: ilastik/multicut | |
- profile: "conda" | |
tags: ilastik/pixelclassification | |
- profile: "conda" | |
tags: imputeme/vcftoprs | |
- profile: "conda" | |
tags: merquryfk/katcomp | |
- profile: "conda" | |
tags: merquryfk/katgc | |
- profile: "conda" | |
tags: merquryfk/merquryfk | |
- profile: "conda" | |
tags: merquryfk/ploidyplot | |
- profile: "conda" | |
tags: sentieon/bwaindex | |
- profile: "conda" | |
tags: sentieon/bwamem | |
- profile: "conda" | |
tags: svanalyzer/svbenchmark | |
- profile: "conda" | |
tags: universc | |
- profile: "singularity" | |
tags: universc | |
- profile: "conda" | |
tags: vt/decompose | |
- profile: "conda" | |
tags: subworkflows/vcf_annotate_ensemblvep | |
env: | |
NXF_ANSI_LOG: false | |
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | |
NFTEST_VER: "0.8.2" | |
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 | |
pip install pdiff | |
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 tests/modules/nf-core/sentieon/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 $SENTIEON_AUTH_DATA_BASE64 | |
# Test the module | |
- name: Run nf-test | |
env: | |
NFT_DIFF: "pdiff" | |
NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
run: | | |
NXF_TEST_DIR=~ \ | |
nf-test test \ | |
--profile=${{ matrix.profile }} \ | |
--tag ${{ matrix.tags }} \ | |
--tap=test.tap \ | |
--verbose | |
- uses: pcolby/tap-summary@v1 | |
with: | |
path: >- | |
test.tap | |
confirm-pass: | |
runs-on: ubuntu-latest | |
needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test] | |
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) }}" |