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main.yml
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name: Tests
on:
push:
branches: [ master ]
pull_request:
branches_ignore: []
jobs:
Formatting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
# Full git history is needed to get a proper
# list of changed files within `super-linter`
fetch-depth: 0
- name: Formatting
uses: github/super-linter@v5
env:
VALIDATE_ALL_CODEBASE: false
DEFAULT_BRANCH: master
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
VALIDATE_SNAKEMAKE_SNAKEFMT: true
Linting:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Lint workflow
uses: snakemake/snakemake-github-action@v1
with:
directory: .
snakefile: workflow/Snakefile
stagein: "mamba install -y -n snakemake --channel conda-forge pyarrow=6.0"
args: "--lint"
Dryrun_Tests:
runs-on: ubuntu-latest
needs:
- Linting
- Formatting
steps:
- uses: actions/checkout@v2
- name: Test workflow (local FASTQs)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
- name: Test testcase generation
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs, target regions)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs, multiple target regions BED files)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs, no candidate filtering)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-no-candidate-filtering/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs primer)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
- name: Test workflow (SRA FASTQs)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-sra/config.yaml --show-failed-logs --use-conda --cores all --set-scatter calling=4 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
Quick_Tests:
runs-on: ubuntu-latest
needs:
- Dryrun_Tests
steps:
- name: update apt
run: sudo apt-get update
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
with:
# this might remove tools that are actually needed,
# if set to "true" but frees about 6 GB
tool-cache: false
# all of these default to true, but feel free to set to
# "false" if necessary for your workflow
android: true
dotnet: true
haskell: true
large-packages: true
docker-images: false
swap-storage: true
- uses: actions/checkout@v2
- name: Test workflow (local FASTQs)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true
- name: Test testcase generation
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "results/testcases/one/freebayes/IX:314200 --configfile .test/config-simple/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true
- name: Test report
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-simple/config.yaml --cores 1 --report report.zip"
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs, target regions)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
stagein: |
rm -rf .test/results
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs, multiple target regions BED files)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-target-regions/config_multiple_beds.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
stagein: |
rm -rf .test/results
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs, no candidate filtering)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-no-candidate-filtering/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
stagein: |
rm -rf .test/results
show-disk-usage-on-error: true
- name: Test workflow (local FASTQs primer)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config_primers/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
stagein: |
rm -rf .test/results
show-disk-usage-on-error: true
Long_Tests:
runs-on: ubuntu-latest
needs:
- Dryrun_Tests
steps:
- name: update apt
run: sudo apt-get update
- name: Free Disk Space (Ubuntu)
uses: jlumbroso/[email protected]
with:
# this might remove tools that are actually needed,
# if set to "true" but frees about 6 GB
tool-cache: false
# all of these default to true, but feel free to set to
# "false" if necessary for your workflow
android: true
dotnet: true
haskell: true
large-packages: true
docker-images: false
swap-storage: true
- uses: actions/checkout@v2
- name: Test workflow (SRA FASTQs)
uses: snakemake/snakemake-github-action@v1
with:
directory: .test
snakefile: workflow/Snakefile
args: "--configfile .test/config-sra/config.yaml --show-failed-logs --use-conda --cores all --set-scatter calling=4 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true