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Merge pull request #176 from Plant-Food-Research-Open/dev
Release 2.2.0
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@@ -49,3 +49,4 @@ indent_style = unset | |
# ignore perl | ||
[*.{pl,pm}] | ||
indent_size = unset | ||
indent_style = unset |
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".": | ||
- ./.github/workflows/** | ||
- ./nf-test.config | ||
tests: | ||
- ./assets/* | ||
- ./bin/* | ||
- ./conf/* | ||
- ./main.nf | ||
- ./nextflow_schema.json | ||
- ./nextflow.config |
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@@ -1,88 +1,100 @@ | ||
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] | ||
|
||
env: | ||
NXF_ANSI_LOG: false | ||
NFT_WORKDIR: "~" | ||
NFT_DIFF: "pdiff" | ||
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | ||
|
||
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 == 'plant-food-research-open/assemblyqc') }}" | ||
nf-test-changes: | ||
name: Check for changes | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
NXF_VER: | ||
- "23.04.0" | ||
TEST_PARAMS: | ||
- minimal | ||
- invalid | ||
- stub | ||
- noltr | ||
- hicparam | ||
include: | ||
- OPTION_STUB: "" | ||
- OPTION_STUB: "-stub" | ||
TEST_PARAMS: stub | ||
- OPTION_STUB: "-stub" | ||
TEST_PARAMS: hicparam | ||
outputs: | ||
nf_test_files: ${{ steps.list.outputs.components }} | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
|
||
- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v2 | ||
- uses: actions/checkout@v4.2.1 | ||
with: | ||
version: ${{ matrix.NXF_VER }} | ||
fetch-depth: 0 | ||
|
||
- name: Disk space cleanup | ||
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
- name: List nf-test files | ||
id: list | ||
uses: adamrtalbot/detect-nf-test-changes@v0.0.4 | ||
with: | ||
head: ${{ github.sha }} | ||
base: origin/${{ github.base_ref }} | ||
include: .github/include.yaml | ||
|
||
- name: Run pipeline with test data | ||
- name: print list of nf-test files | ||
run: | | ||
nextflow run \ | ||
${GITHUB_WORKSPACE} \ | ||
--outdir ./results \ | ||
-profile docker \ | ||
-params-file \ | ||
./tests/${{ matrix.TEST_PARAMS }}/params.json \ | ||
${{ matrix.OPTION_STUB }} | ||
echo ${{ steps.list.outputs.components }} | ||
nf-test: | ||
name: Run nf-tests | ||
# Only run on push if this is the nf-core dev branch (merged PRs) | ||
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'plant-food-research-open/assemblyqc') }}" | ||
test: | ||
name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} | ||
needs: [nf-test-changes] | ||
if: needs.nf-test-changes.outputs.nf_test_files != '[]' | ||
runs-on: ubuntu-latest | ||
strategy: | ||
fail-fast: false | ||
matrix: | ||
NXF_VER: | ||
- "23.04.0" | ||
- "24.04.2" | ||
|
||
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | ||
profile: | ||
- "docker" | ||
|
||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
uses: actions/checkout@v4.2.1 | ||
|
||
- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v2 | ||
with: | ||
version: ${{ matrix.NXF_VER }} | ||
version: "${{ matrix.NXF_VER }}" | ||
|
||
- uses: actions/setup-python@v5.2.0 | ||
with: | ||
python-version: "3.11" | ||
architecture: "x64" | ||
|
||
- name: Install pdiff to see diff between nf-test snapshots | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install pdiff | ||
- uses: nf-core/setup-nf-test@v1.1.2 | ||
with: | ||
version: 0.9.0 | ||
|
||
- name: Install nf-test | ||
uses: nf-core/setup-nf-test@v1.1.2 | ||
- name: Disk space cleanup | ||
if: matrix.nf_test_files == 'tests/stub/main.nf.test' | ||
uses: jlumbroso/free-disk-space@v1.3.1 | ||
|
||
- name: Run nf-test | ||
run: | | ||
nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" | ||
confirm-pass: | ||
runs-on: ubuntu-latest | ||
needs: [test] | ||
if: always() | ||
steps: | ||
- name: All tests ok | ||
if: ${{ !contains(needs.*.result, 'failure') }} | ||
run: exit 0 | ||
- name: One or more tests failed | ||
if: ${{ contains(needs.*.result, 'failure') }} | ||
run: exit 1 | ||
|
||
- name: Run nf-tests | ||
- name: debug-print | ||
if: always() | ||
run: | | ||
nf-test \ | ||
test \ | ||
--verbose \ | ||
tests | ||
echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |
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