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main.yaml
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name: Tests
on:
push:
paths:
- "**/Snakefile"
- "**/*.smk"
- "**/*.py"
- ".github/workflows/*"
jobs:
Testing_local-fastq:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (Local Fastq > VCF)
uses: snakemake/snakemake-github-action@v1.25.1
with:
directory: .test/ecoli/
snakefile: workflow/Snakefile
args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
stagein: "conda config --set channel_priority strict"
Testing_config-genomes:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (Local Fastq > VCF)
uses: snakemake/snakemake-github-action@v1.25.1
with:
directory: .test/ecoli/
snakefile: workflow/Snakefile
args: "--config samples='config/ecoli_config_genome.csv' refGenome='ecoli' refPath='data/local_genome/local_genome.fna.gz' --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
Testing_local-fastq-sentieon-dryrun:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (Local Fastq > VCF)
uses: snakemake/snakemake-github-action@v1.25.1
with:
directory: .test/ecoli/
snakefile: workflow/Snakefile
args: "--config sentieon=True --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba --dry-run"
stagein: "conda config --set channel_priority strict"
Testing_local-fastq_and_sra:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (Local Fastq > VCF)
uses: snakemake/snakemake-github-action@v1.25.1
with:
directory: .test/ecoli/
snakefile: workflow/Snakefile
args: "--config samples='config/local_and_sra.csv' --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
Testing_QC:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (QC rules)
uses: snakemake/snakemake-github-action@v1.25.1
with:
snakefile: workflow/modules/qc/Snakefile
directory: .test/qc/
args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
# stagein: "mamba install -y -c conda-forge 'python==3.11.4'"
Testing_Postprocess:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (Postprocess)
uses: snakemake/snakemake-github-action@v1.25.1
with:
snakefile: workflow/modules/postprocess/Snakefile
directory: .test/postprocess/
args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
# stagein: "mamba install -y -c conda-forge 'python==3.11.4'"
Testing_Trackhub:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Test workflow (Trackhubs)
uses: snakemake/snakemake-github-action@v1.25.1
with:
snakefile: workflow/modules/trackhub/Snakefile
directory: .test/trackhub/
args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba"
# stagein: "mamba install -y -c conda-forge 'python==3.11.4'"