Add MetaEuk for Eukaryotic genome annotation #1187
Workflow file for this run
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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 | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
test: | |
name: Run pipeline with test data | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
steps: | |
- name: Free some space | |
run: | | |
sudo rm -rf "/usr/local/share/boost" | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
- name: Check out pipeline code | |
uses: actions/checkout@v3 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: Run pipeline with test data | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results | |
profiles: | |
name: Run workflow profile | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
# Run remaining test profiles with minimum nextflow version | |
profile: | |
[ | |
test_host_rm, | |
test_hybrid, | |
test_hybrid_host_rm, | |
test_busco_auto, | |
test_ancient_dna, | |
test_adapterremoval, | |
test_binrefinement, | |
test_virus_identification, | |
] | |
steps: | |
- name: Free some space | |
run: | | |
sudo rm -rf "/usr/local/share/boost" | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with ${{ matrix.profile }} test profile | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results | |
checkm: | |
name: Run single test to checkm due to database download | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/mag') }} | |
runs-on: ubuntu-latest | |
steps: | |
- name: Free some space | |
run: | | |
sudo rm -rf "/usr/local/share/boost" | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Download and prepare CheckM database | |
run: | | |
mkdir -p databases/checkm | |
wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz -P databases/checkm | |
tar xzvf databases/checkm/checkm_data_2015_01_16.tar.gz -C databases/checkm/ | |
- name: Run pipeline with ${{ matrix.profile }} test profile | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --binqc_tool checkm --checkm_db databases/checkm |