Update docs #4778
Workflow file for this run
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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] | |
# Cancel if a newer run is started | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
cancel-in-progress: true | |
jobs: | |
test: | |
name: Run pipeline with test data | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
# HACK Remove after DSL2 rewrite is done | |
fail-fast: false | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
test: | |
- "default" | |
profile: ["docker"] | |
# profile: ["docker", "singularity", "conda"] | |
env: | |
NXF_ANSI_LOG: false | |
TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v3 | |
- name: Hash Github Workspace | |
id: hash_workspace | |
run: | | |
echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT | |
- name: Cache test data | |
id: cache-testdata | |
uses: actions/cache@v3 | |
with: | |
path: test-datasets/ | |
key: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: sarek3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in tests/csv/3.0/*csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/modules/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: "3.x" | |
- uses: actions/cache@v3 | |
with: | |
path: ~/.cache/pip | |
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
restore-keys: | | |
${{ runner.os }}-pip- | |
- name: Install Python dependencies | |
run: python -m pip install --upgrade pip pytest-workflow | |
- uses: actions/cache@v3 | |
with: | |
path: /usr/local/bin/nextflow | |
key: ${{ runner.os }} | |
restore-keys: | | |
${{ runner.os }}-nextflow- | |
- name: Install Nextflow ${{ matrix.NXF_VER }} | |
uses: nf-core/setup-nextflow@v1.2.0 | |
with: | |
version: "${{ 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: ${{ matrix.python-version }} | |
- name: Conda clean | |
if: matrix.profile == 'conda' | |
run: conda clean -a | |
- name: Run pipeline with tests settings | |
uses: Wandalen/wretry.action@v1.0.11 | |
with: | |
command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes | |
attempt_limit: 3 | |
- name: Output log on failure | |
if: failure() | |
run: | | |
sudo apt install bat > /dev/null | |
batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} | |
- name: Upload logs on failure | |
if: failure() | |
uses: actions/upload-artifact@v2 | |
with: | |
name: logs-${{ 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 |