Skip to content

Commit

Permalink
CI: try nf-test shard from nascent
Browse files Browse the repository at this point in the history
  • Loading branch information
sateeshperi committed Sep 10, 2024
1 parent 3c66d2d commit d2a5273
Show file tree
Hide file tree
Showing 2 changed files with 32 additions and 66 deletions.
10 changes: 10 additions & 0 deletions .github/include.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
".":
- ./.github/workflows/**
- ./nf-test.config
- ./nextflow.config
tests:
- ./assets/*
- ./bin/*
- ./conf/*
- ./main.nf
- ./nextflow_schema.json
88 changes: 22 additions & 66 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -1,7 +1,12 @@
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
Expand All @@ -13,52 +18,21 @@ env:
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.components }}
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0

- name: List nf-test files
id: list
uses: adamrtalbot/[email protected]
with:
head: ${{ github.sha }}
base: origin/${{ github.base_ref }}
include: .github/include.yaml

- name: print list of nf-test files
run: |
echo ${{ steps.list.outputs.components }}

jobs:
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:
- "latest-everything"
- "23.04"
nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
profile:
- "docker"

shard: [1, 2, 3, 4]
NXF_VER: ["latest-stable"] # TODO Test minimum version on release
profile: ["docker"]
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
fetch-depth: 0

- uses: actions/setup-python@v4
with:
Expand All @@ -70,43 +44,25 @@ jobs:
python -m pip install --upgrade pip
pip install pdiff
- uses: nf-core/setup-nf-test@v1

- name: Run nf-test
run: |
nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
- uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

- uses: pcolby/tap-summary@v1
- uses: nf-core/setup-nf-test@v1
with:
path: >-
test.tap
version: ${{ env.NFT_VER }}

- name: Output log on failure
if: failure()
- name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
nf-test test \
--ci \
--shard ${{ matrix.shard }}/${{ strategy.job-total }} \
--changed-since HEAD^ \
--profile "+${{ matrix.profile }}" \
--filter pipeline
- 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: ${{ !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) }}"

0 comments on commit d2a5273

Please sign in to comment.