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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: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
vg_deconstruct:
name: Run pipeline with vg deconstruct parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- '--vcf_spec "gi|568815561:#,gi|568815567:#"'
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"
- name: Run pipeline with test data and vg deconstruct parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
smoothxg:
name: Run pipeline with smoothxg parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--smoothxg_write_maf --smoothxg_poa_length 100,200,300 --smoothxg_run_abpoa --smoothxg_run_global_poa"
- "--smoothxg_poa_params asm10"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"
- name: Run pipeline with test data and smoothxg parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
wfmash_chunks:
name: Run pipeline with wfmash_chunks parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--wfmash_chunks 2"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"
- name: Run pipeline with test data and wfmash_chunks parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
wfmash_only:
name: Run pipeline with wfmash_only parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--wfmash_only"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"
- name: Run pipeline with test data and wfmash_only parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
wfmash_sparse_map:
name: Run pipeline with wfmash_sparse_map parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--wfmash_sparse_map auto"
- "--wfmash_sparse_map 0.5"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"
- name: Run pipeline with test data and wfmash_only parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
communities:
name: Run pipeline with community parameters
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}"
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--communities"
- "--communities --wfmash_chunks 2"
- '--communities --vcf_spec "gi|568815561:#,gi|568815567:#"'
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "23.04.0"
- name: Run pipeline with test data and wfmash_only parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}