New checkpoint + check counts & SNP nb to bypass cells & chrom #149
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: MosaiCatcher assemblies checks | |
| on: | |
| schedule: | |
| # Run every Sunday at 00:00 UTC on the master branch | |
| - cron: "0 0 * * 0" | |
| # branches: | |
| # - master | |
| push: | |
| branches: | |
| - "*" | |
| - "!master" | |
| jobs: | |
| # Downloading_example_data: | |
| # runs-on: ubuntu-latest | |
| # # needs: | |
| # # - Linting | |
| # # - Formatting | |
| # steps: | |
| # - uses: actions/checkout@v3.3.0 | |
| # - name: Downloading_example_data | |
| # uses: snakemake/snakemake-github-action@v1.24.0 | |
| # with: | |
| # directory: . | |
| # snakefile: ./workflow/Snakefile | |
| # stagein: "mamba install -c conda-forge unzip" | |
| # args: "--cores 1 --config dl_bam_example=True -p --verbose --debug" | |
| Downloading_hg19: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Linting | |
| # - Formatting | |
| steps: | |
| - uses: actions/checkout@v3.3.0 | |
| - name: Downloading hg19 | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| stagein: "conda config --set channel_priority flexible" | |
| args: "--cores 1 --use-conda --conda-frontend mamba --config reference=hg19 -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_hg19.ok" | |
| Downloading_hg38: | |
| runs-on: ubuntu-latest # needs: | |
| # - Linting | |
| # - Formatting | |
| steps: | |
| - uses: actions/checkout@v3.3.0 | |
| - name: Downloading hg38 | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| stagein: "conda config --set channel_priority flexible" | |
| args: "--cores 1 --use-conda --conda-frontend mamba --config reference=hg38 -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_hg38.ok" | |
| Downloading_T2T: | |
| runs-on: ubuntu-latest # needs: | |
| # - Linting | |
| # - Formatting | |
| steps: | |
| - uses: actions/checkout@v3.3.0 | |
| - name: Downloading T2T | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| stagein: "conda config --set channel_priority flexible" | |
| args: "--cores 1 --use-conda --conda-frontend mamba --latency-wait 60 --config reference=T2T -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_T2T.ok" | |
| Downloading_mm10: | |
| runs-on: ubuntu-latest # needs: | |
| # - Linting | |
| # - Formatting | |
| steps: | |
| - uses: actions/checkout@v3.3.0 | |
| - name: Downloading T2T | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: . | |
| snakefile: ./workflow/Snakefile | |
| stagein: "conda config --set channel_priority flexible" | |
| args: "--cores 1 --use-conda --conda-frontend mamba --latency-wait 60 --config reference=mm10 -p --verbose --debug workflow/data/ref_genomes/config/BSgenome_mm10.ok" |