2.2.1: fixes #93
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| 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/[email protected] | |
| # - name: Downloading_example_data | |
| # uses: snakemake/[email protected] | |
| # 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/[email protected] | |
| - name: Downloading hg19 | |
| uses: snakemake/[email protected] | |
| 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/[email protected] | |
| - name: Downloading hg38 | |
| uses: snakemake/[email protected] | |
| 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/[email protected] | |
| - name: Downloading T2T | |
| uses: snakemake/[email protected] | |
| 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/[email protected] | |
| - name: Downloading T2T | |
| uses: snakemake/[email protected] | |
| 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" |