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Important! Template update for nf-core/tools v3.0.2 #223

Important! Template update for nf-core/tools v3.0.2

Important! Template update for nf-core/tools v3.0.2 #223

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]
workflow_dispatch:
env:
NFT_DIFF: "pdiff"
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
NFT_VER: "0.8.4"
NFT_WORKDIR: "~"
NXF_ANSI_LOG: false
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-changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
nf_test_files: ${{ steps.list.outputs.nf_test_files }}
steps:
- uses: actions/setup-python@v4
with:
python-version: "3.11"
architecture: "x64"
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
pip install gitpython pyyaml
- name: list nf_test_files
id: list
run: |
echo nf_test_files=$(python \
.github/python/find_changed_files.py \
-t pipeline workflow process \
--head_ref ${{ github.sha }} \
--base_ref origin/${{ github.base_ref }} \
) >> $GITHUB_OUTPUT
- name: debug
run: |
echo ${{ steps.list.outputs.nf_test_files }}
test:
name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.nf_test_files }} | ${{ matrix.profile }})"
needs: [nf-test-changes]
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/riboseq') && needs.nf-test-changes.outputs.nf_test_files != '[]')}}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
profile:
- "conda"
- "docker"
- "singularity"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
exclude:
- isMaster: false
profile: "conda"
- isMaster: false
profile: "singularity"
- nf_test_files: "subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test"
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 nf-test
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: Cache pdiff
uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
id: cache-pip-pdiff
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-pdiff
- name: Set up pdiff to see diff between nf-test snapshots
run: |
python -m pip install --upgrade pip
pip install pdiff cryptography
- 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: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run nf-test
run: |
nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap
- 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
confirm-pass:
runs-on: ubuntu-latest
needs: [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) }}"