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ci.yml
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# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
name: nf-core CI
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
workflow_dispatch:
env:
NXF_ANSI_LOG: false
NFT_VER: "0.9.0"
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test_profile_standard:
name: nf-test with standard profiles
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
profile:
# - "conda"
- "docker"
- "singularity"
test_name:
- "test"
- "test_model_information"
- "test_mouse_all_pep_lengths"
- "test_assembly_only"
- "test_bins_only"
- "test_coassembly"
- "test_mhcflurry"
- "test_mhcnuggets_1"
- "test_mhcnuggets_2"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
exclude:
# - isMaster: false
# profile: "conda"
- isMaster: false
profile: "singularity"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Set up Apptainer
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-apptainer@main
- name: Set up Singularity
if: matrix.profile == 'singularity'
run: |
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR
- name: Set up Miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
with:
miniconda-version: "latest"
auto-update-conda: true
conda-solver: libmamba
channels: conda-forge,bioconda
- name: Set up Conda
if: matrix.profile == 'conda'
run: |
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH
- name: Clean up Disk space
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: ${{ env.NFT_VER }}
- name: Run nf-test
run: |
nf-test test --tag ${{ matrix.test_name }} --profile ${{ matrix.test_name }},${{ matrix.profile }} --junitxml=test.xml --verbose
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: "*.xml"
test_profile_download:
name: nf-test with profiles needing entrez downloads
# Only run on PRs from branches of nf-core/metapep repository or on push if this is the nf-core dev branch (merged PRs)
# (GitHub secrets are not accessible for workflows from forks)
if: "${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
profile:
# - "conda"
- "docker"
- "singularity"
test_name:
- "test_all"
- "test_mouse"
- "test_taxa_only"
- "test_taxa_specific_assembly"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
exclude:
# - isMaster: false
# profile: "conda"
- isMaster: false
profile: "singularity"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Set up Apptainer
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-apptainer@main
- name: Set up Singularity
if: matrix.profile == 'singularity'
run: |
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR
- name: Set up Miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
with:
miniconda-version: "latest"
auto-update-conda: true
conda-solver: libmamba
channels: conda-forge,bioconda
- name: Set up Conda
if: matrix.profile == 'conda'
run: |
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH
- name: Clean up Disk space
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: ${{ env.NFT_VER }}
- name: Run nf-test
env:
NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }}
NCBI_KEY: ${{ secrets.NCBI_KEY }}
run: |
nextflow secrets set NCBI_EMAIL ${{ secrets.NCBI_EMAIL }}
nextflow secrets set NCBI_KEY ${{ secrets.NCBI_KEY }}
nf-test test --tag ${{ matrix.test_name }} --profile ${{ matrix.test_name }},${{ matrix.profile }} --junitxml=test.xml --verbose
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: "*.xml"