update git stuff #407
Workflow file for this run
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| name: Tests | ||
| on: | ||
| push: | ||
| paths: | ||
| - "*/Snakefile" | ||
| - "*.smk" | ||
| - "*.py" | ||
| paths-ignore: | ||
| - "config/**" | ||
| - "**.md" | ||
| - "profiles/**" | ||
| 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 | ||
| with: | ||
| directory: .test/ecoli/ | ||
| snakefile: workflow/Snakefile | ||
| args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba" | ||
| 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 | ||
| 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 | ||
| with: | ||
| snakefile: workflow/modules/qc/Snakefile | ||
| directory: .test/qc/ | ||
| args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba" | ||
| Testing_Postprocess: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Test workflow (Postprocess) | ||
| uses: snakemake/snakemake-github-action@v1 | ||
| with: | ||
| snakefile: workflow/modules/postprocess/Snakefile | ||
| directory: .test/postprocess/ | ||
| args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba" | ||
| Testing_Trackhub: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Test workflow (Trackhubs) | ||
| uses: snakemake/snakemake-github-action@v1 | ||
| with: | ||
| snakefile: workflow/modules/trackhub/Snakefile | ||
| directory: .test/trackhub/ | ||
| args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba" | ||
