add logs for concat gvcf and normalise #460
Workflow file for this run
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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'" |