Adding script to download blast nt viral database #70
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: tests | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Dry_Run_and_Lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: docker://snakemake/snakemake:v5.24.2 | |
| - name: Dry Run with Paired-end | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/metavirs run --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ | |
| /opt2/.tests/WT_S2_R1.fastq.gz /opt2/.tests/WT_S2_R2.fastq.gz \ | |
| /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz /opt2/.tests/WT_S4_R2.001.fastq.gz \ | |
| --output /opt2/output --mode local --aggregate --dry-run | |
| - name: Dry Run with Single-end | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/metavirs run --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz \ | |
| /opt2/.tests/WT_S2_R1.fastq.gz \ | |
| /opt2/.tests/WT_S3_1.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz \ | |
| --output /opt2/output --mode local --aggregate --dry-run | |
| - name: Dry Run with Mixed | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \ | |
| /opt2/metavirs run --input \ | |
| /opt2/.tests/WT_S1.R1.fastq.gz /opt2/.tests/WT_S1.R2.fastq.gz \ | |
| /opt2/.tests/WT_S2_R1.fastq.gz \ | |
| /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \ | |
| /opt2/.tests/WT_S4_R1.001.fastq.gz \ | |
| --output /opt2/output --mode local --aggregate --dry-run | |
| - name: View the pipeline config file | |
| run: | | |
| echo "Generated config file for pipeline...." && cat $PWD/output/config.json | |
| - name: Lint Workflow | |
| continue-on-error: true | |
| run: | | |
| docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \ | |
| echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.' |