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Original file line number | Diff line number | Diff line change |
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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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}" | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
NXF_VER: | ||
- "23.04.0" | ||
- "latest-everything" | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v3 | ||
|
||
- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v1 | ||
with: | ||
version: "${{ matrix.NXF_VER }}" | ||
|
||
- name: Run pipeline with complete test data | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test_full,docker --outdir ./results --max_cpus 2 --max_memory 4GB |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,40 @@ | ||
name: nf-core CI | ||
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
on: | ||
push: | ||
branches: | ||
- dev | ||
pull_request: | ||
release: | ||
types: [published] | ||
|
||
env: | ||
NXF_ANSI_LOG: false | ||
|
||
concurrency: | ||
group: "${{ 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/viralgenie') }}" | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
NXF_VER: | ||
- "23.04.0" | ||
- "latest-everything" | ||
steps: | ||
- 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 umi test data | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test_umi,docker --outdir ./results --max_cpus 2 --max_memory 4GB |