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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]
workflow_dispatch:
env:
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/multiplesequencealign') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "24.04.2"
- "latest-everything"
profile:
- "conda"
- "docker"
- "singularity"
test_name:
- "test"
- "test_pdb"
- "test_nosheet"
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
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: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
test_conda:
name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/multiplesequencealign') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "24.10.4"
- "latest-everything"
profile:
- "conda"
test_name:
- "test_conda"
- "test_pdb"
- "test_nosheet"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
#exclude:
# - isMaster: false
# profile: "conda"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Set up 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: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
parameters_stub:
name: Stub run
# 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/multiplesequencealign') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "24.10.4"
- "latest-everything"
profile:
- "conda"
- "docker"
- "singularity"
params:
- "--skip_stats"
- "--skip_eval"
- "--skip_visualisation"
- "--skip_validation"
- "--skip_preprocessing"
- "--skip_compression"
- "--skip_shiny"
test_name:
- "test"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
exclude:
- isMaster: false
profile: "conda"
- isMaster: false
profile: "singularity"
steps:
- name: Check out pipeline code
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
fetch-depth: 0
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ 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: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} ${{ matrix.params }} --outdir ./results