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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
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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'Joon-Klaps/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
VARIANT_CALLER:
- "bcftools"
- "ivar"
CONSENSUS_CALLER:
- "bcftools"
- "ivar"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with small test data with variant caller ${{ matrix.VARIANT_CALLER }} and consensus caller ${{ matrix.CONSENSUS_CALLER }}
env:
VARIANT_CALLER: ${{ matrix.VARIANT_CALLER }}
CONSENSUS_CALLER: ${{ matrix.CONSENSUS_CALLER }}
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --variant_caller ${VARIANT_CALLER} --consensus_caller ${CONSENSUS_CALLER} --outdir ./results --max_cpus 2 --max_memory 4GB
test-full:
name: Run complete pipeline with more test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run complete pipeline with more test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_full,docker --outdir ./results --max_cpus 4 --max_memory 15GB
test-umi:
name: Run pipeline with test umi data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with umi test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_umi,docker --outdir ./results --max_cpus 2 --max_memory 4GB
test-nothing:
name: Run pipeline and skip everything
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline but skip all steps
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --outdir ./results --max_cpus 2 --max_memory 4GB
test-fail-mapped:
name: Run pipeline with test bad mapping constrained reference
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with umi test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_fail_mapped,docker --outdir ./results --max_cpus 2 --max_memory 4GB
test-fail-db:
name: Run pipeline with test bad database for identifying potential references
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data of a bad reference database
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_fail_db,docker --outdir ./results --max_cpus 2 --max_memory 4GB
test-cluster-methods:
name: Run pipeline with minimal test data and different cluster methods
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "latest-everything"
CLUSTER_METHOD:
- "vsearch"
- "mmseqs-cluster"
- "mmseqs-linclust"
- "mash"
- "vrhyme"
- "cdhitest"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data and cluster using ${{ matrix.CLUSTER_METHOD }}
env:
CLUSTER_METHOD: ${{ matrix.CLUSTER_METHOD }}
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --cluster_method ${CLUSTER_METHOD} --skip_iterative_refinement --skip_variant_calling --outdir ./results --max_cpus 4 --max_memory 15GB