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Empty ref to samtools sort #205

Empty ref to samtools sort

Empty ref to samtools sort #205

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:
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
NFT_VER: "0.8.4"
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:
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: ${{ 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: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"]
profile:
- "docker"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- uses: actions/setup-python@v4
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
- name: Cache nf-test installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
- name: Install nf-test
if: steps.cache-software.outputs.cache-hit != 'true'
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash
sudo mv nf-test /usr/local/bin/
- 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) }}"