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Merge pull request #112 from Plant-Food-Research-Open/dev
Candidate for 0.5.0
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,10 @@ | ||
".": | ||
- ./.github/workflows/** | ||
- ./nf-test.config | ||
tests: | ||
- ./assets/* | ||
- ./bin/* | ||
- ./conf/* | ||
- ./main.nf | ||
- ./nextflow_schema.json | ||
- ./nextflow.config |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,8 +1,24 @@ | ||
#!/usr/bin/env bash | ||
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config_version=$(sed -n "s/.*version.*= '\(.*\)'.*/\1/p" nextflow.config) | ||
set -euo pipefail | ||
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# Check CHANGELOG version | ||
config_version=$(sed -n "/^\s*version\s*=\s*'/s/version//p" nextflow.config | tr -d "=[:space:]'") | ||
cff_version=$(sed -n '/^version: /s/version: //p' CITATION.cff | tr -d '[:space:]') | ||
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if [[ $config_version != $cff_version ]]; then | ||
echo 'config_version != cff_version' | ||
exit 1 | ||
fi | ||
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head -n 10 CHANGELOG.md | grep "## $config_version - " >/dev/null \ | ||
# Check CHANGELOG version | ||
head -10 CHANGELOG.md | grep "## v$config_version - " >/dev/null \ | ||
|| (echo 'Failed to match CHANGELOG version'; exit 1) | ||
|
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# Check .nf-core.yml version | ||
tail -5 .nf-core.yml | grep "version: $config_version" >/dev/null \ | ||
|| (echo 'Failed to match .nf-core.yml version'; exit 1) | ||
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# Check multiqc_config.yml version | ||
config_version_plain=$(echo $config_version | sed 's/.*\dev$/dev/; t; s/\+.*//') | ||
head -n 5 assets/multiqc_config.yml | grep "https://github.com/plant-food-research-open/genepal/blob/$config_version_plain/docs/usage.md" >/dev/null \ | ||
|| (echo 'Failed to match multiqc_config.yml version'; exit 1) |
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Original file line number | Diff line number | Diff line change |
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@@ -1,58 +1,100 @@ | ||
name: nf-core CI | ||
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
on: | ||
push: | ||
branches: | ||
- dev | ||
pull_request: | ||
release: | ||
types: [published] | ||
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||
env: | ||
NXF_ANSI_LOG: false | ||
NFT_WORKDIR: "nf-test-work" | ||
NFT_DIFF: "pdiff" | ||
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" | ||
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concurrency: | ||
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
cancel-in-progress: true | ||
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jobs: | ||
nf-test-changes: | ||
name: Check for changes | ||
runs-on: ubuntu-latest | ||
outputs: | ||
nf_test_files: ${{ steps.list.outputs.components }} | ||
steps: | ||
- uses: actions/[email protected] | ||
with: | ||
fetch-depth: 0 | ||
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||
- name: List nf-test files | ||
id: list | ||
uses: adamrtalbot/[email protected] | ||
with: | ||
head: ${{ github.sha }} | ||
base: origin/${{ github.base_ref }} | ||
include: .github/include.yaml | ||
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- name: print list of nf-test files | ||
run: | | ||
echo ${{ steps.list.outputs.components }} | ||
test: | ||
name: Run pipeline with test data | ||
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'Plant-Food-Research-Open/genepal') }}" | ||
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" | ||
TEST_PARAMS: | ||
- minimal | ||
- short | ||
- nonmasked | ||
- stub | ||
OPTION_STUB: | ||
- "-stub" | ||
- "24.04.2" | ||
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nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] | ||
profile: | ||
- "docker" | ||
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steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 | ||
uses: actions/checkout@v4.2.1 | ||
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- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v2 | ||
with: | ||
version: "${{ matrix.NXF_VER }}" | ||
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- uses: actions/[email protected] | ||
with: | ||
python-version: "3.11" | ||
architecture: "x64" | ||
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- name: Install pdiff to see diff between nf-test snapshots | ||
run: | | ||
python -m pip install --upgrade pip | ||
pip install pdiff | ||
- uses: nf-core/[email protected] | ||
with: | ||
version: 0.9.0 | ||
|
||
- name: Disk space cleanup | ||
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 | ||
if: matrix.nf_test_files == 'tests/stub/main.nf.test' | ||
uses: jlumbroso/[email protected] | ||
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||
- 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 pipeline with test data | ||
- name: debug-print | ||
if: always() | ||
run: | | ||
nextflow run \ | ||
${GITHUB_WORKSPACE} \ | ||
-profile docker \ | ||
-params-file \ | ||
./tests/${{ matrix.TEST_PARAMS }}/params.json \ | ||
${{ matrix.OPTION_STUB }} \ | ||
--outdir ./results \ | ||
--max_cpus 2 \ | ||
--max_memory '6.GB' \ | ||
--max_time '2.h' | ||
echo "toJSON(needs) = ${{ toJSON(needs) }}" | ||
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |
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