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Update docs #4778

Workflow file for this run

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