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ci.yml
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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_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:
star_salmon:
name: Test STAR Salmon with workflow parameters
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc"
- "--skip_trimming"
- "--min_mapped_reads 90"
- "--with_umi"
- "--with_umi --skip_trimming"
- "--remove_ribo_rna --skip_qualimap"
- "--bam_csi_index"
- "--save_align_intermeds --save_reference"
- "--featurecounts_group_type false"
- "--trimmer fastp"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Setup Nextflow
uses: nf-core/[email protected]
- name: Run pipeline with STAR and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
star_rsem:
name: Test STAR RSEM with workflow parameters
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Setup Nextflow
uses: nf-core/[email protected]
- name: Run pipeline with RSEM STAR and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
hisat2:
name: Test HISAT2 with workflow parameters
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Setup Nextflow
uses: nf-core/[email protected]
- name: Run pipeline with HISAT2 and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
pseudo:
name: Test Pseudoaligners with workflow parameters
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--pseudo_aligner salmon --skip_qc"
- "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
- "--pseudo_aligner kallisto --skip_qc"
- "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Setup Nextflow
uses: nf-core/[email protected]
- name: Run pipeline with Salmon or Kallisto and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
nf-test-changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
changes: ${{ steps.changed_files.outputs.any_modified }}
tags: ${{ steps.list.outputs.tags }}
steps:
- uses: actions/setup-python@v4
with:
python-version: "3.11"
architecture: "x64"
- uses: actions/checkout@v4
with:
fetch-depth: 0
- uses: tj-actions/changed-files@v42
id: changed_files
with:
dir_names: "true"
output_renamed_files_as_deleted_and_added: "true"
# Define list of additional rules for testing paths
# Mostly, we define additional 'pipeline' or 'all' tests here
files_yaml: |
".":
- .github/workflows/**
- nf-test.config
- nextflow.config
tests:
- assets/*
- bin/*
- conf/*
- main.nf
- nextflow_schema.json
files_ignore: |
.git*
.gitpod.yml
.prettierignore
.prettierrc.yml
**.md
**.png
modules.json
pyproject.toml
tower.yml
- name: print-changed-dirs
run: |
echo ${{ steps.changed_files.outputs.any_modified }}
echo ${{ steps.changed_files.outputs.all_changed_files }}
echo ${{ steps.changed_files.outputs.changed_keys }}
- name: nf-test list tags
id: list
if: ${{ steps.changed_files.outputs.any_modified }}
run: |
echo tags=$(python \
.github/python/find_changed_files.py \
-t pipeline workflow process \
-p ${{ steps.changed_files.outputs.all_changed_files }} ${{ steps.changed_files.outputs.changed_keys }} \
) >> $GITHUB_OUTPUT
- name: print-test-tags
run: |
echo ${{ steps.list.outputs.tags }}
test:
name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
needs: [nf-test-changes]
if: needs.nf-test-changes.outputs.tags != '[]'
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
# - "latest-everything"
- "23.04.0"
tags: ["${{ fromJson(needs.nf-test-changes.outputs.tags) }}"]
profile:
- "docker"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Setup Nextflow
uses: nf-core/[email protected]
with:
version: "${{ 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 --tag ${{ matrix.tags }} --profile "+${{ 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, star_salmon, star_rsem, hisat2, pseudo]
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 ${{ needs.nf-test-changes.outputs.changes }}
echo "toJSON(needs) = ${{ toJSON(needs) }}"
echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"